I: pbuilder: network access will be disabled during build I: Current time: Mon Jan 22 02:24:39 -12 2024 I: pbuilder-time-stamp: 1705933479 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/bookworm-reproducible-base.tgz] I: copying local configuration W: --override-config is not set; not updating apt.conf Read the manpage for details. I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: using eatmydata during job I: Copying source file I: copying [openstructure_2.3.1-9.dsc] I: copying [./openstructure_2.3.1.orig.tar.gz] I: copying [./openstructure_2.3.1-9.debian.tar.xz] I: Extracting source gpgv: Signature made Wed May 24 04:59:49 2023 gpgv: using RSA key 772292F6F7AC85FAE041D41EE5F43F9C2734F287 gpgv: issuer "merkys@debian.org" gpgv: Can't check signature: No public key dpkg-source: warning: cannot verify inline signature for ./openstructure_2.3.1-9.dsc: no acceptable signature found dpkg-source: info: extracting openstructure in openstructure-2.3.1 dpkg-source: info: unpacking openstructure_2.3.1.orig.tar.gz dpkg-source: info: unpacking openstructure_2.3.1-9.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying python-dist-packages.patch dpkg-source: info: applying fix-quotes-in-ENV.patch dpkg-source: info: applying skip-network-tests.patch dpkg-source: info: applying ost-compare-structures.patch dpkg-source: info: applying ost_config.patch dpkg-source: info: applying skip-dssp-tests.patch dpkg-source: info: applying 86c621b68f23f98fc30ed230be222ce4dd9432cd.patch dpkg-source: info: applying b2798f24c37cb2ff0f46b929a4d41b4f3ce54a68.patch I: Not using root during the build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/31460/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build/reproducible-path' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='i386' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 ' DISTRIBUTION='bookworm' HOME='/root' HOST_ARCH='i386' IFS=' ' INVOCATION_ID='28ad98c8be3543d7a2ae973079762040' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' LD_LIBRARY_PATH='/usr/lib/libeatmydata' LD_PRELOAD='libeatmydata.so' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='31460' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/r-b-build.glzFcvK4/pbuilderrc_tmON --distribution bookworm --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/bookworm-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/r-b-build.glzFcvK4/b1 --logfile b1/build.log openstructure_2.3.1-9.dsc' SUDO_GID='112' SUDO_UID='107' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://78.137.99.97:3128' I: uname -a Linux ionos2-i386 6.1.0-17-686-pae #1 SMP PREEMPT_DYNAMIC Debian 6.1.69-1 (2023-12-30) i686 GNU/Linux I: ls -l /bin total 6036 -rwxr-xr-x 1 root root 1408088 Apr 23 2023 bash -rwxr-xr-x 3 root root 38404 Sep 19 2022 bunzip2 -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzcat lrwxrwxrwx 1 root root 6 Sep 19 2022 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2225 Sep 19 2022 bzdiff lrwxrwxrwx 1 root root 6 Sep 19 2022 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4893 Nov 27 2021 bzexe lrwxrwxrwx 1 root root 6 Sep 19 2022 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3775 Sep 19 2022 bzgrep -rwxr-xr-x 3 root root 38404 Sep 19 2022 bzip2 -rwxr-xr-x 1 root root 17892 Sep 19 2022 bzip2recover lrwxrwxrwx 1 root root 6 Sep 19 2022 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Sep 19 2022 bzmore -rwxr-xr-x 1 root root 42920 Sep 20 2022 cat -rwxr-xr-x 1 root root 79816 Sep 20 2022 chgrp -rwxr-xr-x 1 root root 67496 Sep 20 2022 chmod -rwxr-xr-x 1 root root 79816 Sep 20 2022 chown -rwxr-xr-x 1 root root 162024 Sep 20 2022 cp -rwxr-xr-x 1 root root 136916 Jan 5 2023 dash -rwxr-xr-x 1 root root 137160 Sep 20 2022 date -rwxr-xr-x 1 root root 100364 Sep 20 2022 dd -rwxr-xr-x 1 root root 108940 Sep 20 2022 df -rwxr-xr-x 1 root root 162152 Sep 20 2022 dir -rwxr-xr-x 1 root root 87760 Mar 23 2023 dmesg lrwxrwxrwx 1 root root 8 Dec 19 2022 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Dec 19 2022 domainname -> hostname -rwxr-xr-x 1 root root 38760 Sep 20 2022 echo -rwxr-xr-x 1 root root 41 Jan 24 2023 egrep -rwxr-xr-x 1 root root 34664 Sep 20 2022 false -rwxr-xr-x 1 root root 41 Jan 24 2023 fgrep -rwxr-xr-x 1 root root 84272 Mar 23 2023 findmnt -rwsr-xr-x 1 root root 30240 Mar 23 2023 fusermount -rwxr-xr-x 1 root root 218680 Jan 24 2023 grep -rwxr-xr-x 2 root root 2346 Apr 10 2022 gunzip -rwxr-xr-x 1 root root 6447 Apr 10 2022 gzexe -rwxr-xr-x 1 root root 100952 Apr 10 2022 gzip -rwxr-xr-x 1 root root 21916 Dec 19 2022 hostname -rwxr-xr-x 1 root root 75756 Sep 20 2022 ln -rwxr-xr-x 1 root root 55600 Mar 23 2023 login -rwxr-xr-x 1 root root 162152 Sep 20 2022 ls -rwxr-xr-x 1 root root 214568 Mar 23 2023 lsblk -rwxr-xr-x 1 root root 96328 Sep 20 2022 mkdir -rwxr-xr-x 1 root root 84008 Sep 20 2022 mknod -rwxr-xr-x 1 root root 38792 Sep 20 2022 mktemp -rwxr-xr-x 1 root root 63016 Mar 23 2023 more -rwsr-xr-x 1 root root 58912 Mar 23 2023 mount -rwxr-xr-x 1 root root 13856 Mar 23 2023 mountpoint -rwxr-xr-x 1 root root 157932 Sep 20 2022 mv lrwxrwxrwx 1 root root 8 Dec 19 2022 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Apr 3 2023 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 38792 Sep 20 2022 pwd lrwxrwxrwx 1 root root 4 Apr 23 2023 rbash -> bash -rwxr-xr-x 1 root root 51080 Sep 20 2022 readlink -rwxr-xr-x 1 root root 75720 Sep 20 2022 rm -rwxr-xr-x 1 root root 51080 Sep 20 2022 rmdir -rwxr-xr-x 1 root root 22308 Jul 28 23:46 run-parts -rwxr-xr-x 1 root root 133224 Jan 5 2023 sed lrwxrwxrwx 1 root root 4 Jan 5 2023 sh -> dash -rwxr-xr-x 1 root root 38760 Sep 20 2022 sleep -rwxr-xr-x 1 root root 87976 Sep 20 2022 stty -rwsr-xr-x 1 root root 83492 Mar 23 2023 su -rwxr-xr-x 1 root root 38792 Sep 20 2022 sync -rwxr-xr-x 1 root root 598456 Apr 6 2023 tar -rwxr-xr-x 1 root root 13860 Jul 28 23:46 tempfile -rwxr-xr-x 1 root root 120776 Sep 20 2022 touch -rwxr-xr-x 1 root root 34664 Sep 20 2022 true -rwxr-xr-x 1 root root 17892 Mar 23 2023 ulockmgr_server -rwsr-xr-x 1 root root 30236 Mar 23 2023 umount -rwxr-xr-x 1 root root 38760 Sep 20 2022 uname -rwxr-xr-x 2 root root 2346 Apr 10 2022 uncompress -rwxr-xr-x 1 root root 162152 Sep 20 2022 vdir -rwxr-xr-x 1 root root 71216 Mar 23 2023 wdctl lrwxrwxrwx 1 root root 8 Dec 19 2022 ypdomainname -> hostname -rwxr-xr-x 1 root root 1984 Apr 10 2022 zcat -rwxr-xr-x 1 root root 1678 Apr 10 2022 zcmp -rwxr-xr-x 1 root root 6460 Apr 10 2022 zdiff -rwxr-xr-x 1 root root 29 Apr 10 2022 zegrep -rwxr-xr-x 1 root root 29 Apr 10 2022 zfgrep -rwxr-xr-x 1 root root 2081 Apr 10 2022 zforce -rwxr-xr-x 1 root root 8103 Apr 10 2022 zgrep -rwxr-xr-x 1 root root 2206 Apr 10 2022 zless -rwxr-xr-x 1 root root 1842 Apr 10 2022 zmore -rwxr-xr-x 1 root root 4577 Apr 10 2022 znew I: user script /srv/workspace/pbuilder/31460/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: i386 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: clustalw, cmake, debhelper-compat (= 13), dh-python, dssp, libboost-all-dev, libeigen3-dev, libfftw3-dev, libglu1-mesa-dev, libpng-dev, libqt5opengl5-dev, libsqlite3-dev, libtiff-dev, python3-dev, python3-matplotlib, python3-numpy, python3-pil, python3-pyqt5, python3-scipy, qtbase5-dev, sip-dev, voronota dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18156 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 clustalw; however: Package clustalw is not installed. pbuilder-satisfydepends-dummy depends on cmake; however: Package cmake is not installed. pbuilder-satisfydepends-dummy depends on debhelper-compat (= 13); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on dssp; however: Package dssp is not installed. pbuilder-satisfydepends-dummy depends on libboost-all-dev; however: Package libboost-all-dev is not installed. pbuilder-satisfydepends-dummy depends on libeigen3-dev; however: Package libeigen3-dev is not installed. pbuilder-satisfydepends-dummy depends on libfftw3-dev; however: Package libfftw3-dev is not installed. pbuilder-satisfydepends-dummy depends on libglu1-mesa-dev; however: Package libglu1-mesa-dev is not installed. pbuilder-satisfydepends-dummy depends on libpng-dev; however: Package libpng-dev is not installed. pbuilder-satisfydepends-dummy depends on libqt5opengl5-dev; however: Package libqt5opengl5-dev is not installed. pbuilder-satisfydepends-dummy depends on libsqlite3-dev; however: Package libsqlite3-dev is not installed. pbuilder-satisfydepends-dummy depends on libtiff-dev; however: Package libtiff-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-dev; however: Package python3-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-pil; however: Package python3-pil is not installed. pbuilder-satisfydepends-dummy depends on python3-pyqt5; however: Package python3-pyqt5 is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on qtbase5-dev; however: Package qtbase5-dev is not installed. pbuilder-satisfydepends-dummy depends on sip-dev; however: Package sip-dev is not installed. pbuilder-satisfydepends-dummy depends on voronota; however: Package voronota is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} blt{a} bsdextrautils{a} clustalw{a} cmake{a} cmake-data{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dssp{a} dwz{a} file{a} fontconfig{a} fontconfig-config{a} fonts-dejavu-core{a} fonts-lyx{a} gettext{a} gettext-base{a} gfortran-12{a} groff-base{a} ibverbs-providers{a} icu-devtools{a} intltool-debian{a} libarchive-zip-perl{a} libarchive13{a} libavahi-client3{a} libavahi-common-data{a} libavahi-common3{a} libblas3{a} libboost-all-dev{a} libboost-atomic-dev{a} libboost-atomic1.74-dev{a} libboost-atomic1.74.0{a} libboost-chrono-dev{a} libboost-chrono1.74-dev{a} libboost-chrono1.74.0{a} libboost-container-dev{a} libboost-container1.74-dev{a} libboost-container1.74.0{a} libboost-context-dev{a} libboost-context1.74-dev{a} libboost-context1.74.0{a} libboost-coroutine-dev{a} libboost-coroutine1.74-dev{a} libboost-coroutine1.74.0{a} libboost-date-time-dev{a} libboost-date-time1.74-dev{a} libboost-date-time1.74.0{a} libboost-dev{a} libboost-exception-dev{a} libboost-exception1.74-dev{a} libboost-fiber-dev{a} libboost-fiber1.74-dev{a} libboost-fiber1.74.0{a} libboost-filesystem-dev{a} libboost-filesystem1.74-dev{a} libboost-filesystem1.74.0{a} libboost-graph-dev{a} libboost-graph-parallel-dev{a} libboost-graph-parallel1.74-dev{a} libboost-graph-parallel1.74.0{a} libboost-graph1.74-dev{a} libboost-graph1.74.0{a} libboost-iostreams-dev{a} libboost-iostreams1.74-dev{a} libboost-locale-dev{a} libboost-locale1.74-dev{a} libboost-locale1.74.0{a} libboost-log-dev{a} libboost-log1.74-dev{a} libboost-log1.74.0{a} libboost-math-dev{a} libboost-math1.74-dev{a} libboost-math1.74.0{a} libboost-mpi-dev{a} libboost-mpi-python-dev{a} libboost-mpi-python1.74-dev{a} libboost-mpi-python1.74.0{a} libboost-mpi1.74-dev{a} libboost-mpi1.74.0{a} libboost-nowide-dev{a} libboost-nowide1.74-dev{a} libboost-nowide1.74.0{a} libboost-numpy-dev{a} libboost-numpy1.74-dev{a} libboost-numpy1.74.0{a} libboost-program-options-dev{a} libboost-program-options1.74-dev{a} libboost-program-options1.74.0{a} libboost-python-dev{a} libboost-python1.74-dev{a} libboost-python1.74.0{a} libboost-random-dev{a} libboost-random1.74-dev{a} libboost-random1.74.0{a} libboost-regex-dev{a} libboost-regex1.74-dev{a} libboost-regex1.74.0{a} libboost-serialization-dev{a} libboost-serialization1.74-dev{a} libboost-serialization1.74.0{a} libboost-stacktrace-dev{a} libboost-stacktrace1.74-dev{a} libboost-stacktrace1.74.0{a} libboost-system-dev{a} libboost-system1.74-dev{a} libboost-system1.74.0{a} libboost-test-dev{a} libboost-test1.74-dev{a} libboost-test1.74.0{a} libboost-thread-dev{a} libboost-thread1.74-dev{a} libboost-thread1.74.0{a} libboost-timer-dev{a} libboost-timer1.74-dev{a} libboost-timer1.74.0{a} libboost-tools-dev{a} libboost-type-erasure-dev{a} libboost-type-erasure1.74-dev{a} libboost-type-erasure1.74.0{a} libboost-wave-dev{a} libboost-wave1.74-dev{a} libboost-wave1.74.0{a} libboost1.74-dev{a} libboost1.74-tools-dev{a} libbrotli1{a} libbsd0{a} libcbor0.8{a} libcifpp-data{a} libcifpp5{a} libcups2{a} libcurl4{a} libdbus-1-3{a} libdebhelper-perl{a} libdeflate-dev{a} libdeflate0{a} libdouble-conversion3{a} libdrm-amdgpu1{a} libdrm-common{a} libdrm-intel1{a} libdrm-nouveau2{a} libdrm-radeon1{a} libdrm2{a} libedit2{a} libegl-dev{a} libegl-mesa0{a} libegl1{a} libeigen3-dev{a} libelf1{a} libevdev2{a} libevent-2.1-7{a} libevent-core-2.1-7{a} libevent-dev{a} libevent-extra-2.1-7{a} libevent-openssl-2.1-7{a} libevent-pthreads-2.1-7{a} libexpat1{a} libexpat1-dev{a} libfabric1{a} libfftw3-bin{a} libfftw3-dev{a} libfftw3-double3{a} libfftw3-long3{a} libfftw3-quad3{a} libfftw3-single3{a} libfido2-1{a} libfile-stripnondeterminism-perl{a} libfontconfig1{a} libfreetype6{a} libfribidi0{a} libgbm1{a} libgfortran-12-dev{a} libgfortran5{a} libgl-dev{a} libgl1{a} libgl1-mesa-dri{a} libglapi-mesa{a} libglib2.0-0{a} libglu1-mesa{a} libglu1-mesa-dev{a} libglvnd0{a} libglx-dev{a} libglx-mesa0{a} libglx0{a} libgraphite2-3{a} libgudev-1.0-0{a} libharfbuzz0b{a} libhwloc-dev{a} libhwloc-plugins{a} libhwloc15{a} libibverbs-dev{a} libibverbs1{a} libice6{a} libicu-dev{a} libicu72{a} libimagequant0{a} libinput-bin{a} libinput10{a} libjbig-dev{a} libjbig0{a} libjpeg-dev{a} libjpeg62-turbo{a} libjpeg62-turbo-dev{a} libjs-jquery{a} libjs-jquery-ui{a} libjs-sphinxdoc{a} libjs-underscore{a} libjsoncpp25{a} liblapack3{a} liblbfgsb0{a} liblcms2-2{a} libldap-2.5-0{a} liblerc-dev{a} liblerc4{a} libllvm15{a} libltdl-dev{a} libltdl7{a} liblzma-dev{a} libmagic-mgc{a} libmagic1{a} libmd4c0{a} libmtdev1{a} libmunge2{a} libnghttp2-14{a} libnl-3-200{a} libnl-3-dev{a} libnl-route-3-200{a} libnl-route-3-dev{a} libnuma-dev{a} libnuma1{a} libopenblas-dev{a} libopenblas-pthread-dev{a} libopenblas0{a} libopenblas0-pthread{a} libopengl-dev{a} libopengl0{a} libopenjp2-7{a} libopenmpi-dev{a} libopenmpi3{a} libpciaccess0{a} libpcre2-16-0{a} libpipeline1{a} libpkgconf3{a} libpmix-dev{a} libpmix2{a} libpng-dev{a} libpng16-16{a} libproc2-0{a} libpsl5{a} libpsm-infinipath1{a} libpthread-stubs0-dev{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.11{a} libpython3.11-dev{a} libpython3.11-minimal{a} libpython3.11-stdlib{a} libqhull-r8.0{a} libqt5concurrent5{a} libqt5core5a{a} libqt5dbus5{a} libqt5designer5{a} libqt5gui5{a} libqt5help5{a} libqt5network5{a} libqt5opengl5{a} libqt5opengl5-dev{a} libqt5printsupport5{a} libqt5sql5{a} libqt5test5{a} libqt5widgets5{a} libqt5xml5{a} libraqm0{a} librdmacm1{a} libreadline8{a} librhash0{a} librtmp1{a} libsasl2-2{a} libsasl2-modules-db{a} libsensors-config{a} libsensors5{a} libsm6{a} libsqlite3-dev{a} libssh2-1{a} libsub-override-perl{a} libtcl8.6{a} libtiff-dev{a} libtiff6{a} libtiffxx6{a} libtk8.6{a} libtool{a} libuchardet0{a} libuv1{a} libvulkan-dev{a} libvulkan1{a} libwacom-common{a} libwacom9{a} libwayland-client0{a} libwayland-server0{a} libwebp-dev{a} libwebp7{a} libwebpdemux2{a} libwebpmux3{a} libx11-6{a} libx11-data{a} libx11-dev{a} libx11-xcb1{a} libxau-dev{a} libxau6{a} libxcb-dri2-0{a} libxcb-dri3-0{a} libxcb-glx0{a} libxcb-icccm4{a} libxcb-image0{a} libxcb-keysyms1{a} libxcb-present0{a} libxcb-randr0{a} libxcb-render-util0{a} libxcb-render0{a} libxcb-shape0{a} libxcb-shm0{a} libxcb-sync1{a} libxcb-util1{a} libxcb-xfixes0{a} libxcb-xinerama0{a} libxcb-xinput0{a} libxcb-xkb1{a} libxcb1{a} libxcb1-dev{a} libxdmcp-dev{a} libxdmcp6{a} libxext-dev{a} libxext6{a} libxfixes3{a} libxft2{a} libxkbcommon-x11-0{a} libxkbcommon0{a} libxml2{a} libxnvctrl0{a} libxrender1{a} libxshmfence1{a} libxsimd-dev{a} libxslt1.1{a} libxss1{a} libxxf86vm1{a} libz3-4{a} libzstd-dev{a} m4{a} man-db{a} media-types{a} mpi-default-bin{a} mpi-default-dev{a} ocl-icd-libopencl1{a} openmpi-bin{a} openmpi-common{a} openssh-client{a} pkg-config{a} pkgconf{a} pkgconf-bin{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-all-dev{a} python3-appdirs{a} python3-attr{a} python3-beniget{a} python3-brotli{a} python3-contourpy{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-fonttools{a} python3-fs{a} python3-gast{a} python3-kiwisolver{a} python3-lib2to3{a} python3-lxml{a} python3-lz4{a} python3-matplotlib{a} python3-minimal{a} python3-mpmath{a} python3-numpy{a} python3-packaging{a} python3-pil{a} python3-pil.imagetk{a} python3-pkg-resources{a} python3-ply{a} python3-pyparsing{a} python3-pyqt5{a} python3-pyqt5.sip{a} python3-pythran{a} python3-scipy{a} python3-six{a} python3-sympy{a} python3-tk{a} python3-tz{a} python3-ufolib2{a} python3.11{a} python3.11-dev{a} python3.11-minimal{a} qt5-qmake{a} qt5-qmake-bin{a} qtbase5-dev{a} qtbase5-dev-tools{a} qtchooser{a} readline-common{a} sensible-utils{a} shared-mime-info{a} sip-dev{a} tk8.6-blt2.5{a} tzdata{a} unicode-data{a} voronota{a} x11-common{a} x11proto-dev{a} xkb-data{a} xorg-sgml-doctools{a} xtrans-dev{a} zlib1g-dev{a} The following packages are RECOMMENDED but will NOT be installed: ca-certificates curl dbus isympy-common javascript-common libarchive-cpio-perl libcoarrays-openmpi-dev libglib2.0-data libldap-common libmail-sendmail-perl libpng-tools libqt5sql5-ibase libqt5sql5-mysql libqt5sql5-odbc libqt5sql5-psql libqt5sql5-sqlite libqt5sql5-tds libqt5svg5 libsasl2-modules lynx mesa-vulkan-drivers psmisc publicsuffix python3-bs4 python3-html5lib python3-olefile python3-sip-dev qt5-gtk-platformtheme qttranslations5-l10n qtwayland5 wget xauth xdg-user-dirs 0 packages upgraded, 428 newly installed, 0 to remove and 0 not upgraded. Need to get 275 MB of archives. After unpacking 1383 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main i386 libpython3.11-minimal i386 3.11.2-6 [813 kB] Get: 2 http://deb.debian.org/debian bookworm/main i386 libexpat1 i386 2.5.0-1 [103 kB] Get: 3 http://deb.debian.org/debian bookworm/main i386 python3.11-minimal i386 3.11.2-6 [2130 kB] Get: 4 http://deb.debian.org/debian bookworm/main i386 python3-minimal i386 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main i386 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main i386 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main i386 libreadline8 i386 8.2-1.3 [171 kB] Get: 8 http://deb.debian.org/debian bookworm/main i386 libpython3.11-stdlib i386 3.11.2-6 [1799 kB] Get: 9 http://deb.debian.org/debian bookworm/main i386 python3.11 i386 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main i386 libpython3-stdlib i386 3.11.2-1+b1 [9308 B] Get: 11 http://deb.debian.org/debian bookworm/main i386 python3 i386 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main i386 tzdata all 2023c-5+deb12u1 [296 kB] Get: 13 http://deb.debian.org/debian bookworm/main i386 libproc2-0 i386 2:4.0.2-3 [63.7 kB] Get: 14 http://deb.debian.org/debian bookworm/main i386 procps i386 2:4.0.2-3 [706 kB] Get: 15 http://deb.debian.org/debian bookworm/main i386 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 16 http://deb.debian.org/debian bookworm/main i386 libmagic-mgc i386 1:5.44-3 [305 kB] Get: 17 http://deb.debian.org/debian bookworm/main i386 libmagic1 i386 1:5.44-3 [114 kB] Get: 18 http://deb.debian.org/debian bookworm/main i386 file i386 1:5.44-3 [42.5 kB] Get: 19 http://deb.debian.org/debian bookworm/main i386 gettext-base i386 0.21-12 [162 kB] Get: 20 http://deb.debian.org/debian bookworm/main i386 libuchardet0 i386 0.0.7-1 [67.9 kB] Get: 21 http://deb.debian.org/debian bookworm/main i386 groff-base i386 1.22.4-10 [932 kB] Get: 22 http://deb.debian.org/debian bookworm/main i386 bsdextrautils i386 2.38.1-5+b1 [90.3 kB] Get: 23 http://deb.debian.org/debian bookworm/main i386 libpipeline1 i386 1.5.7-1 [40.0 kB] Get: 24 http://deb.debian.org/debian bookworm/main i386 man-db i386 2.11.2-2 [1397 kB] Get: 25 http://deb.debian.org/debian bookworm/main i386 libbsd0 i386 0.11.7-2 [121 kB] Get: 26 http://deb.debian.org/debian bookworm/main i386 libedit2 i386 3.1-20221030-2 [97.2 kB] Get: 27 http://deb.debian.org/debian bookworm/main i386 libcbor0.8 i386 0.8.0-2+b1 [29.8 kB] Get: 28 http://deb.debian.org/debian bookworm/main i386 libfido2-1 i386 1.12.0-2+b1 [87.0 kB] Get: 29 http://deb.debian.org/debian bookworm/main i386 openssh-client i386 1:9.2p1-2+deb12u1 [1005 kB] Get: 30 http://deb.debian.org/debian bookworm/main i386 m4 i386 1.4.19-3 [294 kB] Get: 31 http://deb.debian.org/debian bookworm/main i386 autoconf all 2.71-3 [332 kB] Get: 32 http://deb.debian.org/debian bookworm/main i386 autotools-dev all 20220109.1 [51.6 kB] Get: 33 http://deb.debian.org/debian bookworm/main i386 automake all 1:1.16.5-1.3 [823 kB] Get: 34 http://deb.debian.org/debian bookworm/main i386 autopoint all 0.21-12 [495 kB] Get: 35 http://deb.debian.org/debian bookworm/main i386 libtcl8.6 i386 8.6.13+dfsg-2 [1095 kB] Get: 36 http://deb.debian.org/debian bookworm/main i386 libbrotli1 i386 1.0.9-2+b6 [275 kB] Get: 37 http://deb.debian.org/debian bookworm/main i386 libpng16-16 i386 1.6.39-2 [283 kB] Get: 38 http://deb.debian.org/debian bookworm/main i386 libfreetype6 i386 2.12.1+dfsg-5 [410 kB] Get: 39 http://deb.debian.org/debian bookworm/main i386 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 40 http://deb.debian.org/debian bookworm/main i386 fontconfig-config i386 2.14.1-4 [315 kB] Get: 41 http://deb.debian.org/debian bookworm/main i386 libfontconfig1 i386 2.14.1-4 [398 kB] Get: 42 http://deb.debian.org/debian bookworm/main i386 libxau6 i386 1:1.0.9-1 [20.0 kB] Get: 43 http://deb.debian.org/debian bookworm/main i386 libxdmcp6 i386 1:1.1.2-3 [26.7 kB] Get: 44 http://deb.debian.org/debian bookworm/main i386 libxcb1 i386 1.15-1 [148 kB] Get: 45 http://deb.debian.org/debian bookworm/main i386 libx11-data all 2:1.8.4-2+deb12u2 [292 kB] Get: 46 http://deb.debian.org/debian bookworm/main i386 libx11-6 i386 2:1.8.4-2+deb12u2 [782 kB] Get: 47 http://deb.debian.org/debian bookworm/main i386 libxrender1 i386 1:0.9.10-1.1 [34.1 kB] Get: 48 http://deb.debian.org/debian bookworm/main i386 libxft2 i386 2.3.6-1 [62.8 kB] Get: 49 http://deb.debian.org/debian bookworm/main i386 libxext6 i386 2:1.3.4-1+b1 [55.3 kB] Get: 50 http://deb.debian.org/debian bookworm/main i386 x11-common all 1:7.7+23 [252 kB] Get: 51 http://deb.debian.org/debian bookworm/main i386 libxss1 i386 1:1.2.3-1 [18.1 kB] Get: 52 http://deb.debian.org/debian bookworm/main i386 libtk8.6 i386 8.6.13-2 [824 kB] Get: 53 http://deb.debian.org/debian bookworm/main i386 tk8.6-blt2.5 i386 2.5.3+dfsg-4.1 [622 kB] Get: 54 http://deb.debian.org/debian bookworm/main i386 blt i386 2.5.3+dfsg-4.1 [14.9 kB] Get: 55 http://deb.debian.org/debian bookworm/main i386 clustalw i386 2.1+lgpl-7 [302 kB] Get: 56 http://deb.debian.org/debian bookworm/main i386 libicu72 i386 72.1-3 [9541 kB] Get: 57 http://deb.debian.org/debian bookworm/main i386 libxml2 i386 2.9.14+dfsg-1.3~deb12u1 [720 kB] Get: 58 http://deb.debian.org/debian bookworm/main i386 libarchive13 i386 3.6.2-1 [385 kB] Get: 59 http://deb.debian.org/debian bookworm/main i386 libsasl2-modules-db i386 2.1.28+dfsg-10 [21.4 kB] Get: 60 http://deb.debian.org/debian bookworm/main i386 libsasl2-2 i386 2.1.28+dfsg-10 [62.7 kB] Get: 61 http://deb.debian.org/debian bookworm/main i386 libldap-2.5-0 i386 2.5.13+dfsg-5 [196 kB] Get: 62 http://deb.debian.org/debian bookworm/main i386 libnghttp2-14 i386 1.52.0-1+deb12u1 [80.7 kB] Get: 63 http://deb.debian.org/debian bookworm/main i386 libpsl5 i386 0.21.2-1 [59.3 kB] Get: 64 http://deb.debian.org/debian bookworm/main i386 librtmp1 i386 2.4+20151223.gitfa8646d.1-2+b2 [64.3 kB] Get: 65 http://deb.debian.org/debian bookworm/main i386 libssh2-1 i386 1.10.0-3+b1 [187 kB] Get: 66 http://deb.debian.org/debian bookworm/main i386 libcurl4 i386 7.88.1-10+deb12u4 [424 kB] Get: 67 http://deb.debian.org/debian bookworm/main i386 libjsoncpp25 i386 1.9.5-4 [86.2 kB] Get: 68 http://deb.debian.org/debian bookworm/main i386 librhash0 i386 1.4.3-3 [149 kB] Get: 69 http://deb.debian.org/debian bookworm/main i386 libuv1 i386 1.44.2-1 [147 kB] Get: 70 http://deb.debian.org/debian bookworm/main i386 cmake-data all 3.25.1-1 [2026 kB] Get: 71 http://deb.debian.org/debian bookworm/main i386 cmake i386 3.25.1-1 [9767 kB] Get: 72 http://deb.debian.org/debian bookworm/main i386 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 73 http://deb.debian.org/debian bookworm/main i386 libtool all 2.4.7-5 [517 kB] Get: 74 http://deb.debian.org/debian bookworm/main i386 dh-autoreconf all 20 [17.1 kB] Get: 75 http://deb.debian.org/debian bookworm/main i386 libarchive-zip-perl all 1.68-1 [104 kB] Get: 76 http://deb.debian.org/debian bookworm/main i386 libsub-override-perl all 0.09-4 [9304 B] Get: 77 http://deb.debian.org/debian bookworm/main i386 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 78 http://deb.debian.org/debian bookworm/main i386 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 79 http://deb.debian.org/debian bookworm/main i386 libelf1 i386 0.188-2.1 [179 kB] Get: 80 http://deb.debian.org/debian bookworm/main i386 dwz i386 0.15-1 [118 kB] Get: 81 http://deb.debian.org/debian bookworm/main i386 gettext i386 0.21-12 [1311 kB] Get: 82 http://deb.debian.org/debian bookworm/main i386 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 83 http://deb.debian.org/debian bookworm/main i386 po-debconf all 1.0.21+nmu1 [248 kB] Get: 84 http://deb.debian.org/debian bookworm/main i386 debhelper all 13.11.4 [942 kB] Get: 85 http://deb.debian.org/debian bookworm/main i386 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 86 http://deb.debian.org/debian bookworm/main i386 python3-distutils all 3.11.2-3 [131 kB] Get: 87 http://deb.debian.org/debian bookworm/main i386 dh-python all 5.20230130+deb12u1 [104 kB] Get: 88 http://deb.debian.org/debian bookworm/main i386 libboost-regex1.74.0 i386 1.74.0+ds1-21 [509 kB] Get: 89 http://deb.debian.org/debian bookworm/main i386 libcifpp-data all 5.0.7.1-1 [452 kB] Get: 90 http://deb.debian.org/debian bookworm/main i386 libcifpp5 i386 5.0.7.1-1 [856 kB] Get: 91 http://deb.debian.org/debian bookworm/main i386 dssp i386 4.2.2-2 [637 kB] Get: 92 http://deb.debian.org/debian bookworm/main i386 fontconfig i386 2.14.1-4 [450 kB] Get: 93 http://deb.debian.org/debian bookworm/main i386 fonts-lyx all 2.3.7-1 [186 kB] Get: 94 http://deb.debian.org/debian bookworm/main i386 libgfortran5 i386 12.2.0-14 [698 kB] Get: 95 http://deb.debian.org/debian bookworm/main i386 libgfortran-12-dev i386 12.2.0-14 [761 kB] Get: 96 http://deb.debian.org/debian bookworm/main i386 gfortran-12 i386 12.2.0-14 [10.5 MB] Get: 97 http://deb.debian.org/debian bookworm/main i386 libnl-3-200 i386 3.7.0-0.2+b1 [66.2 kB] Get: 98 http://deb.debian.org/debian bookworm/main i386 libnl-route-3-200 i386 3.7.0-0.2+b1 [196 kB] Get: 99 http://deb.debian.org/debian bookworm/main i386 libibverbs1 i386 44.0-2 [65.8 kB] Get: 100 http://deb.debian.org/debian bookworm/main i386 ibverbs-providers i386 44.0-2 [368 kB] Get: 101 http://deb.debian.org/debian bookworm/main i386 icu-devtools i386 72.1-3 [214 kB] Get: 102 http://deb.debian.org/debian bookworm/main i386 libavahi-common-data i386 0.8-10 [107 kB] Get: 103 http://deb.debian.org/debian bookworm/main i386 libavahi-common3 i386 0.8-10 [43.5 kB] Get: 104 http://deb.debian.org/debian bookworm/main i386 libdbus-1-3 i386 1.14.10-1~deb12u1 [215 kB] Get: 105 http://deb.debian.org/debian bookworm/main i386 libavahi-client3 i386 0.8-10 [47.6 kB] Get: 106 http://deb.debian.org/debian bookworm/main i386 libblas3 i386 3.11.0-2 [139 kB] Get: 107 http://deb.debian.org/debian bookworm/main i386 libboost1.74-dev i386 1.74.0+ds1-21 [9508 kB] Get: 108 http://deb.debian.org/debian bookworm/main i386 libboost-dev i386 1.74.0.3 [4548 B] Get: 109 http://deb.debian.org/debian bookworm/main i386 libboost1.74-tools-dev i386 1.74.0+ds1-21 [1510 kB] Get: 110 http://deb.debian.org/debian bookworm/main i386 libboost-tools-dev i386 1.74.0.3 [4508 B] Get: 111 http://deb.debian.org/debian bookworm/main i386 libboost-atomic1.74.0 i386 1.74.0+ds1-21 [221 kB] Get: 112 http://deb.debian.org/debian bookworm/main i386 libboost-atomic1.74-dev i386 1.74.0+ds1-21 [222 kB] Get: 113 http://deb.debian.org/debian bookworm/main i386 libboost-atomic-dev i386 1.74.0.3 [4644 B] Get: 114 http://deb.debian.org/debian bookworm/main i386 libboost-chrono1.74.0 i386 1.74.0+ds1-21 [230 kB] Get: 115 http://deb.debian.org/debian bookworm/main i386 libboost-chrono1.74-dev i386 1.74.0+ds1-21 [237 kB] Get: 116 http://deb.debian.org/debian bookworm/main i386 libboost-chrono-dev i386 1.74.0.3 [4956 B] Get: 117 http://deb.debian.org/debian bookworm/main i386 libboost-container1.74.0 i386 1.74.0+ds1-21 [247 kB] Get: 118 http://deb.debian.org/debian bookworm/main i386 libboost-container1.74-dev i386 1.74.0+ds1-21 [252 kB] Get: 119 http://deb.debian.org/debian bookworm/main i386 libboost-container-dev i386 1.74.0.3 [4812 B] Get: 120 http://deb.debian.org/debian bookworm/main i386 libboost-date-time1.74.0 i386 1.74.0+ds1-21 [218 kB] Get: 121 http://deb.debian.org/debian bookworm/main i386 libboost-serialization1.74.0 i386 1.74.0+ds1-21 [325 kB] Get: 122 http://deb.debian.org/debian bookworm/main i386 libboost-serialization1.74-dev i386 1.74.0+ds1-21 [368 kB] Get: 123 http://deb.debian.org/debian bookworm/main i386 libboost-date-time1.74-dev i386 1.74.0+ds1-21 [226 kB] Get: 124 http://deb.debian.org/debian bookworm/main i386 libboost-system1.74.0 i386 1.74.0+ds1-21 [218 kB] Get: 125 http://deb.debian.org/debian bookworm/main i386 libboost-system1.74-dev i386 1.74.0+ds1-21 [219 kB] Get: 126 http://deb.debian.org/debian bookworm/main i386 libboost-thread1.74.0 i386 1.74.0+ds1-21 [259 kB] Get: 127 http://deb.debian.org/debian bookworm/main i386 libboost-thread1.74-dev i386 1.74.0+ds1-21 [270 kB] Get: 128 http://deb.debian.org/debian bookworm/main i386 libboost-context1.74.0 i386 1.74.0+ds1-21 [219 kB] Get: 129 http://deb.debian.org/debian bookworm/main i386 libboost-context1.74-dev i386 1.74.0+ds1-21 [221 kB] Get: 130 http://deb.debian.org/debian bookworm/main i386 libboost-context-dev i386 1.74.0.3 [4540 B] Get: 131 http://deb.debian.org/debian bookworm/main i386 libboost-coroutine1.74.0 i386 1.74.0+ds1-21 [235 kB] Get: 132 http://deb.debian.org/debian bookworm/main i386 libboost-coroutine1.74-dev i386 1.74.0+ds1-21 [243 kB] Get: 133 http://deb.debian.org/debian bookworm/main i386 libboost-coroutine-dev i386 1.74.0.3 [4612 B] Get: 134 http://deb.debian.org/debian bookworm/main i386 libboost-date-time-dev i386 1.74.0.3 [4332 B] Get: 135 http://deb.debian.org/debian bookworm/main i386 libboost-exception1.74-dev i386 1.74.0+ds1-21 [217 kB] Get: 136 http://deb.debian.org/debian bookworm/main i386 libboost-exception-dev i386 1.74.0.3 [4320 B] Get: 137 http://deb.debian.org/debian bookworm/main i386 libboost-filesystem1.74.0 i386 1.74.0+ds1-21 [264 kB] Get: 138 http://deb.debian.org/debian bookworm/main i386 libboost-filesystem1.74-dev i386 1.74.0+ds1-21 [286 kB] Get: 139 http://deb.debian.org/debian bookworm/main i386 libboost-fiber1.74.0 i386 1.74.0+ds1-21 [243 kB] Get: 140 http://deb.debian.org/debian bookworm/main i386 libboost-fiber1.74-dev i386 1.74.0+ds1-21 [254 kB] Get: 141 http://deb.debian.org/debian bookworm/main i386 libboost-fiber-dev i386 1.74.0.3 [4764 B] Get: 142 http://deb.debian.org/debian bookworm/main i386 libboost-filesystem-dev i386 1.74.0.3 [4368 B] Get: 143 http://deb.debian.org/debian bookworm/main i386 libboost-graph1.74.0 i386 1.74.0+ds1-21 [307 kB] Get: 144 http://deb.debian.org/debian bookworm/main i386 libicu-dev i386 72.1-3 [10.6 MB] Get: 145 http://deb.debian.org/debian bookworm/main i386 libboost-regex1.74-dev i386 1.74.0+ds1-21 [585 kB] Get: 146 http://deb.debian.org/debian bookworm/main i386 libboost-test1.74.0 i386 1.74.0+ds1-21 [461 kB] Get: 147 http://deb.debian.org/debian bookworm/main i386 libboost-test1.74-dev i386 1.74.0+ds1-21 [539 kB] Get: 148 http://deb.debian.org/debian bookworm/main i386 libboost-graph1.74-dev i386 1.74.0+ds1-21 [329 kB] Get: 149 http://deb.debian.org/debian bookworm/main i386 libboost-graph-dev i386 1.74.0.3 [4436 B] Get: 150 http://deb.debian.org/debian bookworm/main i386 libevent-core-2.1-7 i386 2.1.12-stable-8 [139 kB] Get: 151 http://deb.debian.org/debian bookworm/main i386 libevent-pthreads-2.1-7 i386 2.1.12-stable-8 [53.7 kB] Get: 152 http://deb.debian.org/debian bookworm/main i386 libpsm-infinipath1 i386 3.3+20.604758e7-6.2 [177 kB] Get: 153 http://deb.debian.org/debian bookworm/main i386 librdmacm1 i386 44.0-2 [74.6 kB] Get: 154 http://deb.debian.org/debian bookworm/main i386 libfabric1 i386 1.17.0-3 [538 kB] Get: 155 http://deb.debian.org/debian bookworm/main i386 libhwloc15 i386 2.9.0-1 [168 kB] Get: 156 http://deb.debian.org/debian bookworm/main i386 libmunge2 i386 0.5.15-2 [20.3 kB] Get: 157 http://deb.debian.org/debian bookworm/main i386 libpciaccess0 i386 0.17-2 [53.4 kB] Get: 158 http://deb.debian.org/debian bookworm/main i386 libxnvctrl0 i386 525.85.05-3~deb12u1 [13.4 kB] Get: 159 http://deb.debian.org/debian bookworm/main i386 ocl-icd-libopencl1 i386 2.3.1-1 [45.4 kB] Get: 160 http://deb.debian.org/debian bookworm/main i386 libhwloc-plugins i386 2.9.0-1 [17.8 kB] Get: 161 http://deb.debian.org/debian bookworm/main i386 libpmix2 i386 4.2.2-1+deb12u1 [652 kB] Get: 162 http://deb.debian.org/debian bookworm/main i386 libopenmpi3 i386 4.1.4-3+b1 [2183 kB] Get: 163 http://deb.debian.org/debian bookworm/main i386 libboost-mpi1.74.0 i386 1.74.0+ds1-21 [260 kB] Get: 164 http://deb.debian.org/debian bookworm/main i386 libboost-graph-parallel1.74.0 i386 1.74.0+ds1-21 [267 kB] Get: 165 http://deb.debian.org/debian bookworm/main i386 libboost-graph-parallel1.74-dev i386 1.74.0+ds1-21 [272 kB] Get: 166 http://deb.debian.org/debian bookworm/main i386 libboost-graph-parallel-dev i386 1.74.0.3 [4460 B] Get: 167 http://deb.debian.org/debian bookworm/main i386 libboost-iostreams1.74-dev i386 1.74.0+ds1-21 [250 kB] Get: 168 http://deb.debian.org/debian bookworm/main i386 libboost-iostreams-dev i386 1.74.0.3 [4320 B] Get: 169 http://deb.debian.org/debian bookworm/main i386 libboost-locale1.74.0 i386 1.74.0+ds1-21 [471 kB] Get: 170 http://deb.debian.org/debian bookworm/main i386 libboost-locale1.74-dev i386 1.74.0+ds1-21 [584 kB] Get: 171 http://deb.debian.org/debian bookworm/main i386 libboost-locale-dev i386 1.74.0.3 [4660 B] Get: 172 http://deb.debian.org/debian bookworm/main i386 libboost-log1.74.0 i386 1.74.0+ds1-21 [625 kB] Get: 173 http://deb.debian.org/debian bookworm/main i386 libboost-log1.74-dev i386 1.74.0+ds1-21 [823 kB] Get: 174 http://deb.debian.org/debian bookworm/main i386 libboost-log-dev i386 1.74.0.3 [4536 B] Get: 175 http://deb.debian.org/debian bookworm/main i386 libboost-math1.74.0 i386 1.74.0+ds1-21 [438 kB] Get: 176 http://deb.debian.org/debian bookworm/main i386 libboost-math1.74-dev i386 1.74.0+ds1-21 [544 kB] Get: 177 http://deb.debian.org/debian bookworm/main i386 libboost-math-dev i386 1.74.0.3 [4536 B] Get: 178 http://deb.debian.org/debian bookworm/main i386 openmpi-common all 4.1.4-3 [167 kB] Get: 179 http://deb.debian.org/debian bookworm/main i386 libnl-3-dev i386 3.7.0-0.2+b1 [109 kB] Get: 180 http://deb.debian.org/debian bookworm/main i386 libnl-route-3-dev i386 3.7.0-0.2+b1 [226 kB] Get: 181 http://deb.debian.org/debian bookworm/main i386 libibverbs-dev i386 44.0-2 [683 kB] Get: 182 http://deb.debian.org/debian bookworm/main i386 libnuma1 i386 2.0.16-1 [22.7 kB] Get: 183 http://deb.debian.org/debian bookworm/main i386 libnuma-dev i386 2.0.16-1 [37.3 kB] Get: 184 http://deb.debian.org/debian bookworm/main i386 libltdl7 i386 2.4.7-5 [394 kB] Get: 185 http://deb.debian.org/debian bookworm/main i386 libltdl-dev i386 2.4.7-5 [167 kB] Get: 186 http://deb.debian.org/debian bookworm/main i386 libhwloc-dev i386 2.9.0-1 [259 kB] Get: 187 http://deb.debian.org/debian bookworm/main i386 libevent-2.1-7 i386 2.1.12-stable-8 [194 kB] Get: 188 http://deb.debian.org/debian bookworm/main i386 libevent-extra-2.1-7 i386 2.1.12-stable-8 [112 kB] Get: 189 http://deb.debian.org/debian bookworm/main i386 libevent-openssl-2.1-7 i386 2.1.12-stable-8 [61.5 kB] Get: 190 http://deb.debian.org/debian bookworm/main i386 libevent-dev i386 2.1.12-stable-8 [325 kB] Get: 191 http://deb.debian.org/debian bookworm/main i386 zlib1g-dev i386 1:1.2.13.dfsg-1 [913 kB] Get: 192 http://deb.debian.org/debian bookworm/main i386 libpmix-dev i386 4.2.2-1+deb12u1 [976 kB] Get: 193 http://deb.debian.org/debian bookworm/main i386 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 194 http://deb.debian.org/debian bookworm/main i386 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 195 http://deb.debian.org/debian bookworm/main i386 openmpi-bin i386 4.1.4-3+b1 [196 kB] Get: 196 http://deb.debian.org/debian bookworm/main i386 libopenmpi-dev i386 4.1.4-3+b1 [920 kB] Get: 197 http://deb.debian.org/debian bookworm/main i386 mpi-default-dev i386 1.14 [5552 B] Get: 198 http://deb.debian.org/debian bookworm/main i386 libboost-mpi1.74-dev i386 1.74.0+ds1-21 [281 kB] Get: 199 http://deb.debian.org/debian bookworm/main i386 libboost-mpi-dev i386 1.74.0.3 [4420 B] Get: 200 http://deb.debian.org/debian bookworm/main i386 libboost-python1.74.0 i386 1.74.0+ds1-21 [295 kB] Get: 201 http://deb.debian.org/debian bookworm/main i386 mpi-default-bin i386 1.14 [4752 B] Get: 202 http://deb.debian.org/debian bookworm/main i386 libboost-mpi-python1.74.0 i386 1.74.0+ds1-21 [343 kB] Get: 203 http://deb.debian.org/debian bookworm/main i386 libboost-mpi-python1.74-dev i386 1.74.0+ds1-21 [225 kB] Get: 204 http://deb.debian.org/debian bookworm/main i386 libboost-mpi-python-dev i386 1.74.0.3 [4456 B] Get: 205 http://deb.debian.org/debian bookworm/main i386 libboost-numpy1.74.0 i386 1.74.0+ds1-21 [229 kB] Get: 206 http://deb.debian.org/debian bookworm/main i386 libboost-numpy1.74-dev i386 1.74.0+ds1-21 [233 kB] Get: 207 http://deb.debian.org/debian bookworm/main i386 libboost-numpy-dev i386 1.74.0.3 [4376 B] Get: 208 http://deb.debian.org/debian bookworm/main i386 libboost-program-options1.74.0 i386 1.74.0+ds1-21 [338 kB] Get: 209 http://deb.debian.org/debian bookworm/main i386 libboost-program-options1.74-dev i386 1.74.0+ds1-21 [369 kB] Get: 210 http://deb.debian.org/debian bookworm/main i386 libboost-program-options-dev i386 1.74.0.3 [4344 B] Get: 211 http://deb.debian.org/debian bookworm/main i386 libpython3.11 i386 3.11.2-6 [2013 kB] Get: 212 http://deb.debian.org/debian bookworm/main i386 libexpat1-dev i386 2.5.0-1 [158 kB] Get: 213 http://deb.debian.org/debian bookworm/main i386 libpython3.11-dev i386 3.11.2-6 [4906 kB] Get: 214 http://deb.debian.org/debian bookworm/main i386 libpython3-dev i386 3.11.2-1+b1 [9580 B] Get: 215 http://deb.debian.org/debian bookworm/main i386 python3.11-dev i386 3.11.2-6 [615 kB] Get: 216 http://deb.debian.org/debian bookworm/main i386 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 217 http://deb.debian.org/debian bookworm/main i386 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 218 http://deb.debian.org/debian bookworm/main i386 python3-dev i386 3.11.2-1+b1 [26.2 kB] Get: 219 http://deb.debian.org/debian bookworm/main i386 libboost-python1.74-dev i386 1.74.0+ds1-21 [319 kB] Get: 220 http://deb.debian.org/debian bookworm/main i386 libboost-python-dev i386 1.74.0.3 [4632 B] Get: 221 http://deb.debian.org/debian bookworm/main i386 libboost-random1.74.0 i386 1.74.0+ds1-21 [228 kB] Get: 222 http://deb.debian.org/debian bookworm/main i386 libboost-random1.74-dev i386 1.74.0+ds1-21 [230 kB] Get: 223 http://deb.debian.org/debian bookworm/main i386 libboost-random-dev i386 1.74.0.3 [4336 B] Get: 224 http://deb.debian.org/debian bookworm/main i386 libboost-regex-dev i386 1.74.0.3 [4596 B] Get: 225 http://deb.debian.org/debian bookworm/main i386 libboost-serialization-dev i386 1.74.0.3 [4560 B] Get: 226 http://deb.debian.org/debian bookworm/main i386 libboost-stacktrace1.74.0 i386 1.74.0+ds1-21 [263 kB] Get: 227 http://deb.debian.org/debian bookworm/main i386 libboost-stacktrace1.74-dev i386 1.74.0+ds1-21 [232 kB] Get: 228 http://deb.debian.org/debian bookworm/main i386 libboost-stacktrace-dev i386 1.74.0.3 [4332 B] Get: 229 http://deb.debian.org/debian bookworm/main i386 libboost-system-dev i386 1.74.0.3 [4472 B] Get: 230 http://deb.debian.org/debian bookworm/main i386 libboost-test-dev i386 1.74.0.3 [4368 B] Get: 231 http://deb.debian.org/debian bookworm/main i386 libboost-thread-dev i386 1.74.0.3 [4356 B] Get: 232 http://deb.debian.org/debian bookworm/main i386 libboost-timer1.74.0 i386 1.74.0+ds1-21 [228 kB] Get: 233 http://deb.debian.org/debian bookworm/main i386 libboost-timer1.74-dev i386 1.74.0+ds1-21 [231 kB] Get: 234 http://deb.debian.org/debian bookworm/main i386 libboost-timer-dev i386 1.74.0.3 [4456 B] Get: 235 http://deb.debian.org/debian bookworm/main i386 libboost-type-erasure1.74.0 i386 1.74.0+ds1-21 [234 kB] Get: 236 http://deb.debian.org/debian bookworm/main i386 libboost-type-erasure1.74-dev i386 1.74.0+ds1-21 [238 kB] Get: 237 http://deb.debian.org/debian bookworm/main i386 libboost-type-erasure-dev i386 1.74.0.3 [4428 B] Get: 238 http://deb.debian.org/debian bookworm/main i386 libboost-wave1.74.0 i386 1.74.0+ds1-21 [421 kB] Get: 239 http://deb.debian.org/debian bookworm/main i386 libboost-wave1.74-dev i386 1.74.0+ds1-21 [486 kB] Get: 240 http://deb.debian.org/debian bookworm/main i386 libboost-wave-dev i386 1.74.0.3 [4360 B] Get: 241 http://deb.debian.org/debian bookworm/main i386 libboost-nowide1.74.0 i386 1.74.0+ds1-21 [219 kB] Get: 242 http://deb.debian.org/debian bookworm/main i386 libboost-nowide1.74-dev i386 1.74.0+ds1-21 [221 kB] Get: 243 http://deb.debian.org/debian bookworm/main i386 libboost-nowide-dev i386 1.74.0.3 [4392 B] Get: 244 http://deb.debian.org/debian bookworm/main i386 libboost-all-dev i386 1.74.0.3 [4676 B] Get: 245 http://deb.debian.org/debian bookworm/main i386 libcups2 i386 2.4.2-3+deb12u5 [262 kB] Get: 246 http://deb.debian.org/debian bookworm/main i386 libdeflate0 i386 1.14-1 [57.5 kB] Get: 247 http://deb.debian.org/debian bookworm/main i386 libdeflate-dev i386 1.14-1 [53.5 kB] Get: 248 http://deb.debian.org/debian bookworm/main i386 libdouble-conversion3 i386 3.2.1-1 [45.7 kB] Get: 249 http://deb.debian.org/debian bookworm/main i386 libdrm-common all 2.4.114-1 [7112 B] Get: 250 http://deb.debian.org/debian bookworm/main i386 libdrm2 i386 2.4.114-1+b1 [40.8 kB] Get: 251 http://deb.debian.org/debian bookworm/main i386 libdrm-amdgpu1 i386 2.4.114-1+b1 [24.1 kB] Get: 252 http://deb.debian.org/debian bookworm/main i386 libdrm-intel1 i386 2.4.114-1+b1 [67.9 kB] Get: 253 http://deb.debian.org/debian bookworm/main i386 libdrm-nouveau2 i386 2.4.114-1+b1 [20.7 kB] Get: 254 http://deb.debian.org/debian bookworm/main i386 libdrm-radeon1 i386 2.4.114-1+b1 [22.8 kB] Get: 255 http://deb.debian.org/debian bookworm/main i386 libglvnd0 i386 1.6.0-1 [42.7 kB] Get: 256 http://deb.debian.org/debian bookworm/main i386 libwayland-server0 i386 1.21.0-1 [37.4 kB] Get: 257 http://deb.debian.org/debian bookworm/main i386 libgbm1 i386 22.3.6-1+deb12u1 [39.2 kB] Get: 258 http://deb.debian.org/debian bookworm/main i386 libglapi-mesa i386 22.3.6-1+deb12u1 [35.6 kB] Get: 259 http://deb.debian.org/debian bookworm/main i386 libwayland-client0 i386 1.21.0-1 [29.0 kB] Get: 260 http://deb.debian.org/debian bookworm/main i386 libx11-xcb1 i386 2:1.8.4-2+deb12u2 [192 kB] Get: 261 http://deb.debian.org/debian bookworm/main i386 libxcb-dri2-0 i386 1.15-1 [107 kB] Get: 262 http://deb.debian.org/debian bookworm/main i386 libxcb-dri3-0 i386 1.15-1 [107 kB] Get: 263 http://deb.debian.org/debian bookworm/main i386 libxcb-present0 i386 1.15-1 [106 kB] Get: 264 http://deb.debian.org/debian bookworm/main i386 libxcb-randr0 i386 1.15-1 [118 kB] Get: 265 http://deb.debian.org/debian bookworm/main i386 libxcb-sync1 i386 1.15-1 [109 kB] Get: 266 http://deb.debian.org/debian bookworm/main i386 libxcb-xfixes0 i386 1.15-1 [110 kB] Get: 267 http://deb.debian.org/debian bookworm/main i386 libxshmfence1 i386 1.3-1 [8976 B] Get: 268 http://deb.debian.org/debian bookworm/main i386 libegl-mesa0 i386 22.3.6-1+deb12u1 [124 kB] Get: 269 http://deb.debian.org/debian bookworm/main i386 libegl1 i386 1.6.0-1 [35.6 kB] Get: 270 http://deb.debian.org/debian bookworm/main i386 libxcb-glx0 i386 1.15-1 [124 kB] Get: 271 http://deb.debian.org/debian bookworm/main i386 libxcb-shm0 i386 1.15-1 [106 kB] Get: 272 http://deb.debian.org/debian bookworm/main i386 libxfixes3 i386 1:6.0.0-2 [23.0 kB] Get: 273 http://deb.debian.org/debian bookworm/main i386 libxxf86vm1 i386 1:1.1.4-1+b2 [21.7 kB] Get: 274 http://deb.debian.org/debian bookworm/main i386 libz3-4 i386 4.8.12-3.1 [7853 kB] Get: 275 http://deb.debian.org/debian bookworm/main i386 libllvm15 i386 1:15.0.6-4+b1 [26.5 MB] Get: 276 http://deb.debian.org/debian bookworm/main i386 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 277 http://deb.debian.org/debian bookworm/main i386 libsensors5 i386 1:3.6.0-7.1 [35.1 kB] Get: 278 http://deb.debian.org/debian bookworm/main i386 libgl1-mesa-dri i386 22.3.6-1+deb12u1 [7417 kB] Get: 279 http://deb.debian.org/debian bookworm/main i386 libglx-mesa0 i386 22.3.6-1+deb12u1 [156 kB] Get: 280 http://deb.debian.org/debian bookworm/main i386 libglx0 i386 1.6.0-1 [36.6 kB] Get: 281 http://deb.debian.org/debian bookworm/main i386 libgl1 i386 1.6.0-1 [82.1 kB] Get: 282 http://deb.debian.org/debian bookworm/main i386 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 283 http://deb.debian.org/debian bookworm/main i386 x11proto-dev all 2022.1-1 [599 kB] Get: 284 http://deb.debian.org/debian bookworm/main i386 libxau-dev i386 1:1.0.9-1 [23.3 kB] Get: 285 http://deb.debian.org/debian bookworm/main i386 libxdmcp-dev i386 1:1.1.2-3 [42.7 kB] Get: 286 http://deb.debian.org/debian bookworm/main i386 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 287 http://deb.debian.org/debian bookworm/main i386 libpthread-stubs0-dev i386 0.4-1 [5340 B] Get: 288 http://deb.debian.org/debian bookworm/main i386 libxcb1-dev i386 1.15-1 [185 kB] Get: 289 http://deb.debian.org/debian bookworm/main i386 libx11-dev i386 2:1.8.4-2+deb12u2 [864 kB] Get: 290 http://deb.debian.org/debian bookworm/main i386 libglx-dev i386 1.6.0-1 [15.3 kB] Get: 291 http://deb.debian.org/debian bookworm/main i386 libgl-dev i386 1.6.0-1 [100 kB] Get: 292 http://deb.debian.org/debian bookworm/main i386 libegl-dev i386 1.6.0-1 [19.1 kB] Get: 293 http://deb.debian.org/debian bookworm/main i386 libpkgconf3 i386 1.8.1-1 [38.3 kB] Get: 294 http://deb.debian.org/debian bookworm/main i386 pkgconf-bin i386 1.8.1-1 [29.8 kB] Get: 295 http://deb.debian.org/debian bookworm/main i386 pkgconf i386 1.8.1-1 [25.9 kB] Get: 296 http://deb.debian.org/debian bookworm/main i386 pkg-config i386 1.8.1-1 [13.7 kB] Get: 297 http://deb.debian.org/debian bookworm/main i386 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 298 http://deb.debian.org/debian bookworm/main i386 libevdev2 i386 1.13.0+dfsg-1 [32.4 kB] Get: 299 http://deb.debian.org/debian bookworm/main i386 libfftw3-double3 i386 3.3.10-1 [633 kB] Get: 300 http://deb.debian.org/debian bookworm/main i386 libfftw3-long3 i386 3.3.10-1 [338 kB] Get: 301 http://deb.debian.org/debian bookworm/main i386 libfftw3-quad3 i386 3.3.10-1 [1795 kB] Get: 302 http://deb.debian.org/debian bookworm/main i386 libfftw3-single3 i386 3.3.10-1 [646 kB] Get: 303 http://deb.debian.org/debian bookworm/main i386 libfftw3-bin i386 3.3.10-1 [50.1 kB] Get: 304 http://deb.debian.org/debian bookworm/main i386 libfftw3-dev i386 3.3.10-1 [3201 kB] Get: 305 http://deb.debian.org/debian bookworm/main i386 libfribidi0 i386 1.0.8-2.1 [65.6 kB] Get: 306 http://deb.debian.org/debian bookworm/main i386 libglib2.0-0 i386 2.74.6-2 [1467 kB] Get: 307 http://deb.debian.org/debian bookworm/main i386 libopengl0 i386 1.6.0-1 [29.2 kB] Get: 308 http://deb.debian.org/debian bookworm/main i386 libglu1-mesa i386 9.0.2-1.1 [186 kB] Get: 309 http://deb.debian.org/debian bookworm/main i386 libopengl-dev i386 1.6.0-1 [4924 B] Get: 310 http://deb.debian.org/debian bookworm/main i386 libglu1-mesa-dev i386 9.0.2-1.1 [230 kB] Get: 311 http://deb.debian.org/debian bookworm/main i386 libgraphite2-3 i386 1.3.14-1 [84.0 kB] Get: 312 http://deb.debian.org/debian bookworm/main i386 libgudev-1.0-0 i386 237-2 [15.7 kB] Get: 313 http://deb.debian.org/debian bookworm/main i386 libharfbuzz0b i386 6.0.0+dfsg-3 [1966 kB] Get: 314 http://deb.debian.org/debian bookworm/main i386 libice6 i386 2:1.0.10-1 [60.8 kB] Get: 315 http://deb.debian.org/debian bookworm/main i386 libimagequant0 i386 2.17.0-1 [32.9 kB] Get: 316 http://deb.debian.org/debian bookworm/main i386 libwacom-common all 2.6.0-1 [58.4 kB] Get: 317 http://deb.debian.org/debian bookworm/main i386 libwacom9 i386 2.6.0-1 [23.1 kB] Get: 318 http://deb.debian.org/debian bookworm/main i386 libinput-bin i386 1.22.1-1 [23.5 kB] Get: 319 http://deb.debian.org/debian bookworm/main i386 libmtdev1 i386 1.1.6-1 [23.5 kB] Get: 320 http://deb.debian.org/debian bookworm/main i386 libinput10 i386 1.22.1-1 [140 kB] Get: 321 http://deb.debian.org/debian bookworm/main i386 libjbig0 i386 2.1-6.1 [31.6 kB] Get: 322 http://deb.debian.org/debian bookworm/main i386 libjbig-dev i386 2.1-6.1 [30.9 kB] Get: 323 http://deb.debian.org/debian bookworm/main i386 libjpeg62-turbo i386 1:2.1.5-2 [169 kB] Get: 324 http://deb.debian.org/debian bookworm/main i386 libjpeg62-turbo-dev i386 1:2.1.5-2 [304 kB] Get: 325 http://deb.debian.org/debian bookworm/main i386 libjpeg-dev i386 1:2.1.5-2 [71.8 kB] Get: 326 http://deb.debian.org/debian bookworm/main i386 libopenblas0-pthread i386 0.3.21+ds-4 [5148 kB] Get: 327 http://deb.debian.org/debian bookworm/main i386 liblapack3 i386 3.11.0-2 [2092 kB] Get: 328 http://deb.debian.org/debian bookworm/main i386 liblbfgsb0 i386 3.0+dfsg.4-1 [28.5 kB] Get: 329 http://deb.debian.org/debian bookworm/main i386 liblcms2-2 i386 2.14-2 [165 kB] Get: 330 http://deb.debian.org/debian bookworm/main i386 liblerc4 i386 4.0.0+ds-2 [181 kB] Get: 331 http://deb.debian.org/debian bookworm/main i386 liblerc-dev i386 4.0.0+ds-2 [193 kB] Get: 332 http://deb.debian.org/debian bookworm/main i386 liblzma-dev i386 5.4.1-0.2 [272 kB] Get: 333 http://deb.debian.org/debian bookworm/main i386 libmd4c0 i386 0.4.8-1 [44.9 kB] Get: 334 http://deb.debian.org/debian bookworm/main i386 libopenblas0 i386 0.3.21+ds-4 [32.6 kB] Get: 335 http://deb.debian.org/debian bookworm/main i386 libopenblas-pthread-dev i386 0.3.21+ds-4 [3447 kB] Get: 336 http://deb.debian.org/debian bookworm/main i386 libopenblas-dev i386 0.3.21+ds-4 [44.9 kB] Get: 337 http://deb.debian.org/debian bookworm/main i386 libopenjp2-7 i386 2.5.0-2 [196 kB] Get: 338 http://deb.debian.org/debian bookworm/main i386 libpcre2-16-0 i386 10.42-1 [243 kB] Get: 339 http://deb.debian.org/debian bookworm/main i386 libpng-dev i386 1.6.39-2 [367 kB] Get: 340 http://deb.debian.org/debian bookworm/main i386 libpython3-all-dev i386 3.11.2-1+b1 [1068 B] Get: 341 http://deb.debian.org/debian bookworm/main i386 libqhull-r8.0 i386 2020.2-5 [260 kB] Get: 342 http://deb.debian.org/debian bookworm/main i386 shared-mime-info i386 2.2-1 [730 kB] Get: 343 http://deb.debian.org/debian bookworm/main i386 libqt5core5a i386 5.15.8+dfsg-11 [2655 kB] Get: 344 http://deb.debian.org/debian bookworm/main i386 libqt5concurrent5 i386 5.15.8+dfsg-11 [42.9 kB] Get: 345 http://deb.debian.org/debian bookworm/main i386 libqt5dbus5 i386 5.15.8+dfsg-11 [235 kB] Get: 346 http://deb.debian.org/debian bookworm/main i386 libqt5network5 i386 5.15.8+dfsg-11 [765 kB] Get: 347 http://deb.debian.org/debian bookworm/main i386 libsm6 i386 2:1.2.3-1 [35.7 kB] Get: 348 http://deb.debian.org/debian bookworm/main i386 libxcb-icccm4 i386 0.4.1-1.1 [28.1 kB] Get: 349 http://deb.debian.org/debian bookworm/main i386 libxcb-util1 i386 0.4.0-1+b1 [23.6 kB] Get: 350 http://deb.debian.org/debian bookworm/main i386 libxcb-image0 i386 0.4.0-2 [23.4 kB] Get: 351 http://deb.debian.org/debian bookworm/main i386 libxcb-keysyms1 i386 0.4.0-1+b2 [16.7 kB] Get: 352 http://deb.debian.org/debian bookworm/main i386 libxcb-render0 i386 1.15-1 [116 kB] Get: 353 http://deb.debian.org/debian bookworm/main i386 libxcb-render-util0 i386 0.3.9-1+b1 [18.7 kB] Get: 354 http://deb.debian.org/debian bookworm/main i386 libxcb-shape0 i386 1.15-1 [106 kB] Get: 355 http://deb.debian.org/debian bookworm/main i386 libxcb-xinerama0 i386 1.15-1 [105 kB] Get: 356 http://deb.debian.org/debian bookworm/main i386 libxcb-xinput0 i386 1.15-1 [134 kB] Get: 357 http://deb.debian.org/debian bookworm/main i386 libxcb-xkb1 i386 1.15-1 [131 kB] Get: 358 http://deb.debian.org/debian bookworm/main i386 xkb-data all 2.35.1-1 [764 kB] Get: 359 http://deb.debian.org/debian bookworm/main i386 libxkbcommon0 i386 1.5.0-1 [112 kB] Get: 360 http://deb.debian.org/debian bookworm/main i386 libxkbcommon-x11-0 i386 1.5.0-1 [16.5 kB] Get: 361 http://deb.debian.org/debian bookworm/main i386 libqt5gui5 i386 5.15.8+dfsg-11 [5894 kB] Get: 362 http://deb.debian.org/debian bookworm/main i386 libqt5widgets5 i386 5.15.8+dfsg-11 [2659 kB] Get: 363 http://deb.debian.org/debian bookworm/main i386 libqt5xml5 i386 5.15.8+dfsg-11 [134 kB] Get: 364 http://deb.debian.org/debian bookworm/main i386 libqt5designer5 i386 5.15.8-2 [2865 kB] Get: 365 http://deb.debian.org/debian bookworm/main i386 libqt5sql5 i386 5.15.8+dfsg-11 [134 kB] Get: 366 http://deb.debian.org/debian bookworm/main i386 libqt5help5 i386 5.15.8-2 [169 kB] Get: 367 http://deb.debian.org/debian bookworm/main i386 libqt5opengl5 i386 5.15.8+dfsg-11 [162 kB] Get: 368 http://deb.debian.org/debian bookworm/main i386 libqt5printsupport5 i386 5.15.8+dfsg-11 [219 kB] Get: 369 http://deb.debian.org/debian bookworm/main i386 libqt5test5 i386 5.15.8+dfsg-11 [152 kB] Get: 370 http://deb.debian.org/debian bookworm/main i386 libvulkan1 i386 1.3.239.0-1 [125 kB] Get: 371 http://deb.debian.org/debian bookworm/main i386 libvulkan-dev i386 1.3.239.0-1 [1115 kB] Get: 372 http://deb.debian.org/debian bookworm/main i386 libxext-dev i386 2:1.3.4-1+b1 [110 kB] Get: 373 http://deb.debian.org/debian bookworm/main i386 qt5-qmake-bin i386 5.15.8+dfsg-11 [1107 kB] Get: 374 http://deb.debian.org/debian bookworm/main i386 qtchooser i386 66-2 [27.8 kB] Get: 375 http://deb.debian.org/debian bookworm/main i386 qt5-qmake i386 5.15.8+dfsg-11 [221 kB] Get: 376 http://deb.debian.org/debian bookworm/main i386 qtbase5-dev-tools i386 5.15.8+dfsg-11 [846 kB] Get: 377 http://deb.debian.org/debian bookworm/main i386 qtbase5-dev i386 5.15.8+dfsg-11 [1122 kB] Get: 378 http://deb.debian.org/debian bookworm/main i386 libqt5opengl5-dev i386 5.15.8+dfsg-11 [49.0 kB] Get: 379 http://deb.debian.org/debian bookworm/main i386 libraqm0 i386 0.7.0-4.1 [11.1 kB] Get: 380 http://deb.debian.org/debian bookworm/main i386 libsqlite3-dev i386 3.40.1-2 [1105 kB] Get: 381 http://deb.debian.org/debian bookworm/main i386 libzstd-dev i386 1.5.4+dfsg2-5 [338 kB] Get: 382 http://deb.debian.org/debian bookworm/main i386 libwebp7 i386 1.2.4-0.2+deb12u1 [294 kB] Get: 383 http://deb.debian.org/debian bookworm/main i386 libwebpmux3 i386 1.2.4-0.2+deb12u1 [111 kB] Get: 384 http://deb.debian.org/debian bookworm/main i386 libwebpdemux2 i386 1.2.4-0.2+deb12u1 [99.8 kB] Get: 385 http://deb.debian.org/debian bookworm/main i386 libwebp-dev i386 1.2.4-0.2+deb12u1 [415 kB] Get: 386 http://deb.debian.org/debian bookworm/main i386 libtiff6 i386 4.5.0-6+deb12u1 [332 kB] Get: 387 http://deb.debian.org/debian bookworm/main i386 libtiffxx6 i386 4.5.0-6+deb12u1 [145 kB] Get: 388 http://deb.debian.org/debian bookworm/main i386 libtiff-dev i386 4.5.0-6+deb12u1 [479 kB] Get: 389 http://deb.debian.org/debian bookworm/main i386 libxsimd-dev i386 8.1.0-7 [88.8 kB] Get: 390 http://deb.debian.org/debian bookworm/main i386 libxslt1.1 i386 1.1.35-1 [253 kB] Get: 391 http://deb.debian.org/debian bookworm/main i386 python-matplotlib-data all 3.6.3-1 [2744 kB] Get: 392 http://deb.debian.org/debian bookworm/main i386 python3-all i386 3.11.2-1+b1 [1056 B] Get: 393 http://deb.debian.org/debian bookworm/main i386 python3-all-dev i386 3.11.2-1+b1 [1072 B] Get: 394 http://deb.debian.org/debian bookworm/main i386 python3-appdirs all 1.4.4-3 [13.0 kB] Get: 395 http://deb.debian.org/debian bookworm/main i386 python3-attr all 22.2.0-1 [65.4 kB] Get: 396 http://deb.debian.org/debian bookworm/main i386 python3-gast all 0.5.2-2 [9364 B] Get: 397 http://deb.debian.org/debian bookworm/main i386 python3-beniget all 0.4.1-3 [9920 B] Get: 398 http://deb.debian.org/debian bookworm/main i386 python3-brotli i386 1.0.9-2+b6 [295 kB] Get: 399 http://deb.debian.org/debian bookworm/main i386 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 400 http://deb.debian.org/debian bookworm/main i386 python3-numpy i386 1:1.24.2-1 [6115 kB] Get: 401 http://deb.debian.org/debian bookworm/main i386 python3-contourpy i386 1.0.7-1+b1 [184 kB] Get: 402 http://deb.debian.org/debian bookworm/main i386 python3-cycler all 0.11.0-1 [8020 B] Get: 403 http://deb.debian.org/debian bookworm/main i386 python3-six all 1.16.0-4 [17.5 kB] Get: 404 http://deb.debian.org/debian bookworm/main i386 python3-dateutil all 2.8.2-2 [78.3 kB] Get: 405 http://deb.debian.org/debian bookworm/main i386 python3-decorator all 5.1.1-3 [14.9 kB] Get: 406 http://deb.debian.org/debian bookworm/main i386 python3-ply all 3.11-5 [65.8 kB] Get: 407 http://deb.debian.org/debian bookworm/main i386 python3-pythran i386 0.11.0+ds-7 [427 kB] Get: 408 http://deb.debian.org/debian bookworm/main i386 python3-scipy i386 1.10.1-2 [15.2 MB] Get: 409 http://deb.debian.org/debian bookworm/main i386 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB] Get: 410 http://deb.debian.org/debian bookworm/main i386 python3-mpmath all 1.2.1-2 [418 kB] Get: 411 http://deb.debian.org/debian bookworm/main i386 python3-sympy all 1.11.1-1 [4358 kB] Get: 412 http://deb.debian.org/debian bookworm/main i386 python3-tz all 2022.7.1-4 [30.1 kB] Get: 413 http://deb.debian.org/debian bookworm/main i386 python3-fs all 2.4.16-2 [95.2 kB] Get: 414 http://deb.debian.org/debian bookworm/main i386 python3-lxml i386 4.9.2-1+b1 [1182 kB] Get: 415 http://deb.debian.org/debian bookworm/main i386 python3-lz4 i386 4.0.2+dfsg-1+b2 [25.1 kB] Get: 416 http://deb.debian.org/debian bookworm/main i386 unicode-data all 15.0.0-1 [7984 kB] Get: 417 http://deb.debian.org/debian bookworm/main i386 python3-fonttools i386 4.38.0-1+b1 [1010 kB] Get: 418 http://deb.debian.org/debian bookworm/main i386 python3-kiwisolver i386 1.4.4-1+b1 [63.0 kB] Get: 419 http://deb.debian.org/debian bookworm/main i386 python3-pil i386 9.4.0-1.1+b1 [473 kB] Get: 420 http://deb.debian.org/debian bookworm/main i386 python3-tk i386 3.11.2-3 [99.2 kB] Get: 421 http://deb.debian.org/debian bookworm/main i386 python3-pil.imagetk i386 9.4.0-1.1+b1 [74.7 kB] Get: 422 http://deb.debian.org/debian bookworm/main i386 python3-pyparsing all 3.0.9-1 [138 kB] Get: 423 http://deb.debian.org/debian bookworm/main i386 python3-packaging all 23.0-1 [32.5 kB] Get: 424 http://deb.debian.org/debian bookworm/main i386 python3-matplotlib i386 3.6.3-1+b1 [6891 kB] Get: 425 http://deb.debian.org/debian bookworm/main i386 python3-pyqt5.sip i386 12.11.1-1 [57.9 kB] Get: 426 http://deb.debian.org/debian bookworm/main i386 python3-pyqt5 i386 5.15.9+dfsg-1 [2254 kB] Get: 427 http://deb.debian.org/debian bookworm/main i386 sip-dev i386 4.19.25+dfsg-5+b1 [256 kB] Get: 428 http://deb.debian.org/debian bookworm/main i386 voronota i386 1.22.3149-2 [2155 kB] Fetched 275 MB in 2min 12s (2092 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:i386. (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 ... 18156 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_i386.deb ... Unpacking libpython3.11-minimal:i386 (3.11.2-6) ... Selecting previously unselected package libexpat1:i386. Preparing to unpack .../libexpat1_2.5.0-1_i386.deb ... Unpacking libexpat1:i386 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_i386.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:i386 (3.11.2-6) ... Setting up libexpat1:i386 (2.5.0-1) ... Setting up python3.11-minimal (3.11.2-6) ... Selecting previously unselected package python3-minimal. (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 ... 18472 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_i386.deb ... Unpacking python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package media-types. Preparing to unpack .../1-media-types_10.0.0_all.deb ... Unpacking media-types (10.0.0) ... Selecting previously unselected package readline-common. Preparing to unpack .../2-readline-common_8.2-1.3_all.deb ... Unpacking readline-common (8.2-1.3) ... Selecting previously unselected package libreadline8:i386. Preparing to unpack .../3-libreadline8_8.2-1.3_i386.deb ... Unpacking libreadline8:i386 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:i386. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_i386.deb ... Unpacking libpython3.11-stdlib:i386 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_i386.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:i386. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_i386.deb ... Unpacking libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up python3-minimal (3.11.2-1+b1) ... Selecting previously unselected package python3. (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 ... 18906 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_i386.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package tzdata. Preparing to unpack .../001-tzdata_2023c-5+deb12u1_all.deb ... Unpacking tzdata (2023c-5+deb12u1) ... Selecting previously unselected package libproc2-0:i386. Preparing to unpack .../002-libproc2-0_2%3a4.0.2-3_i386.deb ... Unpacking libproc2-0:i386 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../003-procps_2%3a4.0.2-3_i386.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../004-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../005-libmagic-mgc_1%3a5.44-3_i386.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:i386. Preparing to unpack .../006-libmagic1_1%3a5.44-3_i386.deb ... Unpacking libmagic1:i386 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../007-file_1%3a5.44-3_i386.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../008-gettext-base_0.21-12_i386.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:i386. Preparing to unpack .../009-libuchardet0_0.0.7-1_i386.deb ... Unpacking libuchardet0:i386 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../010-groff-base_1.22.4-10_i386.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../011-bsdextrautils_2.38.1-5+b1_i386.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:i386. Preparing to unpack .../012-libpipeline1_1.5.7-1_i386.deb ... Unpacking libpipeline1:i386 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../013-man-db_2.11.2-2_i386.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package libbsd0:i386. Preparing to unpack .../014-libbsd0_0.11.7-2_i386.deb ... Unpacking libbsd0:i386 (0.11.7-2) ... Selecting previously unselected package libedit2:i386. Preparing to unpack .../015-libedit2_3.1-20221030-2_i386.deb ... Unpacking libedit2:i386 (3.1-20221030-2) ... Selecting previously unselected package libcbor0.8:i386. Preparing to unpack .../016-libcbor0.8_0.8.0-2+b1_i386.deb ... Unpacking libcbor0.8:i386 (0.8.0-2+b1) ... Selecting previously unselected package libfido2-1:i386. Preparing to unpack .../017-libfido2-1_1.12.0-2+b1_i386.deb ... Unpacking libfido2-1:i386 (1.12.0-2+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../018-openssh-client_1%3a9.2p1-2+deb12u1_i386.deb ... Unpacking openssh-client (1:9.2p1-2+deb12u1) ... Selecting previously unselected package m4. Preparing to unpack .../019-m4_1.4.19-3_i386.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../020-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../021-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../022-automake_1%3a1.16.5-1.3_all.deb ... Unpacking automake (1:1.16.5-1.3) ... Selecting previously unselected package autopoint. Preparing to unpack .../023-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libtcl8.6:i386. Preparing to unpack .../024-libtcl8.6_8.6.13+dfsg-2_i386.deb ... Unpacking libtcl8.6:i386 (8.6.13+dfsg-2) ... Selecting previously unselected package libbrotli1:i386. Preparing to unpack .../025-libbrotli1_1.0.9-2+b6_i386.deb ... Unpacking libbrotli1:i386 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:i386. Preparing to unpack .../026-libpng16-16_1.6.39-2_i386.deb ... Unpacking libpng16-16:i386 (1.6.39-2) ... Selecting previously unselected package libfreetype6:i386. Preparing to unpack .../027-libfreetype6_2.12.1+dfsg-5_i386.deb ... Unpacking libfreetype6:i386 (2.12.1+dfsg-5) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../028-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../029-fontconfig-config_2.14.1-4_i386.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:i386. Preparing to unpack .../030-libfontconfig1_2.14.1-4_i386.deb ... Unpacking libfontconfig1:i386 (2.14.1-4) ... Selecting previously unselected package libxau6:i386. Preparing to unpack .../031-libxau6_1%3a1.0.9-1_i386.deb ... Unpacking libxau6:i386 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:i386. Preparing to unpack .../032-libxdmcp6_1%3a1.1.2-3_i386.deb ... Unpacking libxdmcp6:i386 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:i386. Preparing to unpack .../033-libxcb1_1.15-1_i386.deb ... Unpacking libxcb1:i386 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../034-libx11-data_2%3a1.8.4-2+deb12u2_all.deb ... Unpacking libx11-data (2:1.8.4-2+deb12u2) ... Selecting previously unselected package libx11-6:i386. Preparing to unpack .../035-libx11-6_2%3a1.8.4-2+deb12u2_i386.deb ... Unpacking libx11-6:i386 (2:1.8.4-2+deb12u2) ... Selecting previously unselected package libxrender1:i386. Preparing to unpack .../036-libxrender1_1%3a0.9.10-1.1_i386.deb ... Unpacking libxrender1:i386 (1:0.9.10-1.1) ... Selecting previously unselected package libxft2:i386. Preparing to unpack .../037-libxft2_2.3.6-1_i386.deb ... Unpacking libxft2:i386 (2.3.6-1) ... Selecting previously unselected package libxext6:i386. Preparing to unpack .../038-libxext6_2%3a1.3.4-1+b1_i386.deb ... 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Current default time zone: 'Etc/UTC' Local time is now: Mon Jan 22 14:28:00 UTC 2024. Universal Time is now: Mon Jan 22 14:28:00 UTC 2024. Run 'dpkg-reconfigure tzdata' if you wish to change it. Setting up unicode-data (15.0.0-1) ... Setting up libxsimd-dev:i386 (8.1.0-7) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:i386 (4.8.12-3.1) ... Setting up libblas3:i386 (3.11.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/blas/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode Setting up libpkgconf3:i386 (1.8.1-1) ... Setting up libuv1:i386 (1.44.2-1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libexpat1-dev:i386 (2.5.0-1) ... Setting up libboost-test1.74.0:i386 (1.74.0+ds1-21) ... Setting up libjpeg62-turbo:i386 (1:2.1.5-2) ... Setting up qt5-qmake-bin (5.15.8+dfsg-11) ... Setting up libsqlite3-dev:i386 (3.40.1-2) ... Setting up libboost-program-options-dev:i386 (1.74.0.3) ... Setting up libx11-data (2:1.8.4-2+deb12u2) ... Setting up libjpeg62-turbo-dev:i386 (1:2.1.5-2) ... Setting up librtmp1:i386 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libavahi-common-data:i386 (0.8-10) ... Setting up libboost-system1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libdbus-1-3:i386 (1.14.10-1~deb12u1) ... Setting up libfftw3-quad3:i386 (3.3.10-1) ... Setting up libboost-nowide1.74-dev (1.74.0+ds1-21) ... Setting up libfribidi0:i386 (1.0.8-2.1) ... Setting up libboost-regex1.74.0:i386 (1.74.0+ds1-21) ... Setting up libimagequant0:i386 (2.17.0-1) ... Setting up libproc2-0:i386 (2:4.0.2-3) ... Setting up libpng16-16:i386 (1.6.39-2) ... Setting up libhwloc15:i386 (2.9.0-1) ... Setting up libevent-core-2.1-7:i386 (2.1.12-stable-8) ... Setting up libboost-context1.74.0:i386 (1.74.0+ds1-21) ... Setting up libevent-2.1-7:i386 (2.1.12-stable-8) ... Setting up libboost-graph1.74.0:i386 (1.74.0+ds1-21) ... Setting up libtcl8.6:i386 (8.6.13+dfsg-2) ... Setting up libboost-random1.74.0:i386 (1.74.0+ds1-21) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:i386 (1.9.5-4) ... Setting up icu-devtools (72.1-3) ... Setting up fonts-dejavu-core (2.37-6) ... Setting up libboost1.74-tools-dev (1.74.0+ds1-21) ... Setting up pkgconf-bin (1.8.1-1) ... Setting up libsensors5:i386 (1:3.6.0-7.1) ... Setting up liblerc-dev:i386 (4.0.0+ds-2) ... Setting up libltdl7:i386 (2.4.7-5) ... Setting up libfftw3-double3:i386 (3.3.10-1) ... Setting up libcifpp-data (5.0.7.1-1) ... Setting up libglapi-mesa:i386 (22.3.6-1+deb12u1) ... Setting up libsasl2-2:i386 (2.1.28+dfsg-10) ... Setting up libgfortran5:i386 (12.2.0-14) ... Setting up libmtdev1:i386 (1.1.6-1) ... Setting up libvulkan1:i386 (1.3.239.0-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:i386 (1.2.4-0.2+deb12u1) ... Setting up libboost-atomic1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libboost-math1.74.0:i386 (1.74.0+ds1-21) ... Setting up liblzma-dev:i386 (5.4.1-0.2) ... Setting up libboost-serialization1.74.0:i386 (1.74.0+ds1-21) ... Setting up zlib1g-dev:i386 (1:1.2.13.dfsg-1) ... Setting up libboost-atomic-dev:i386 (1.74.0.3) ... Setting up libnuma1:i386 (2.0.16-1) ... Setting up libboost-container1.74.0:i386 (1.74.0+ds1-21) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up ocl-icd-libopencl1:i386 (2.3.1-1) ... Setting up libxshmfence1:i386 (1.3-1) ... Setting up librhash0:i386 (1.4.3-3) ... Setting up libtiff6:i386 (4.5.0-6+deb12u1) ... Setting up libuchardet0:i386 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libnl-3-200:i386 (3.7.0-0.2+b1) ... Setting up openmpi-common (4.1.4-3) ... Setting up clustalw (2.1+lgpl-7) ... Setting up libmd4c0:i386 (0.4.8-1) ... Setting up libopenjp2-7:i386 (2.5.0-2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:i386 (1.10.0-3+b1) ... Setting up xorg-sgml-doctools (1:1.11-1.1) ... Setting up cmake-data (3.25.1-1) ... Setting up libboost-dev:i386 (1.74.0.3) ... Setting up libglu1-mesa:i386 (9.0.2-1.1) ... Setting up libboost-math1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libpsm-infinipath1 (3.3+20.604758e7-6.2) ... update-alternatives: using /usr/lib/libpsm1/libpsm_infinipath.so.1.16 to provide /usr/lib/i386-linux-gnu/libpsm_infinipath.so.1 (libpsm_infinipath.so.1) in auto mode Setting up libboost-filesystem1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libopengl-dev:i386 (1.6.0-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libboost-date-time1.74.0:i386 (1.74.0+ds1-21) ... Setting up libfido2-1:i386 (1.12.0-2+b1) ... Setting up libboost-python1.74.0 (1.74.0+ds1-21) ... Setting up libboost-fiber1.74.0:i386 (1.74.0+ds1-21) ... Setting up libboost-stacktrace1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libboost-test1.74-dev:i386 (1.74.0+ds1-21) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up libwebpmux3:i386 (1.2.4-0.2+deb12u1) ... Setting up libbsd0:i386 (0.11.7-2) ... Setting up libtiffxx6:i386 (4.5.0-6+deb12u1) ... Setting up libdeflate-dev:i386 (1.14-1) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:i386 (0.188-2.1) ... Setting up libevdev2:i386 (1.13.0+dfsg-1) ... Setting up readline-common (8.2-1.3) ... Setting up libboost-timer1.74.0:i386 (1.74.0+ds1-21) ... Setting up libicu-dev:i386 (72.1-3) ... Setting up libxml2:i386 (2.9.14+dfsg-1.3~deb12u1) ... Setting up libboost-filesystem-dev:i386 (1.74.0.3) ... Setting up libgudev-1.0-0:i386 (237-2) ... Setting up qtchooser (66-2) ... Setting up libjs-underscore (1.13.4~dfsg+~1.11.4-3) ... Setting up libboost-thread1.74.0:i386 (1.74.0+ds1-21) ... Setting up libboost-numpy1.74.0 (1.74.0+ds1-21) ... Setting up libevent-pthreads-2.1-7:i386 (2.1.12-stable-8) ... Setting up libwacom-common (2.6.0-1) ... Setting up libxkbcommon0:i386 (1.5.0-1) ... Setting up libwayland-client0:i386 (1.21.0-1) ... 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 x11proto-dev (2022.1-1) ... Setting up libfile-stripnondeterminism-perl (1.13.1-1) ... Setting up libice6:i386 (2:1.0.10-1) ... Setting up libboost-log1.74.0 (1.74.0+ds1-21) ... Setting up libxdmcp6:i386 (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:i386 (2.1.12-stable-8) ... Setting up liblapack3:i386 (3.11.0-2) ... update-alternatives: using /usr/lib/i386-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode Setting up libxcb1:i386 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libopenblas0-pthread:i386 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/i386-linux-gnu/libblas.so.3 (libblas.so.3-i386-linux-gnu) in auto mode update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/i386-linux-gnu/liblapack.so.3 (liblapack.so.3-i386-linux-gnu) in auto mode update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/i386-linux-gnu/libopenblas.so.0 (libopenblas.so.0-i386-linux-gnu) in auto mode Setting up libxcb-xfixes0:i386 (1.15-1) ... Setting up libxau-dev:i386 (1:1.0.9-1) ... Setting up qt5-qmake:i386 (5.15.8+dfsg-11) ... Setting up libxcb-xinput0:i386 (1.15-1) ... Setting up libtool (2.4.7-5) ... Setting up libboost-container1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libarchive13:i386 (3.6.2-1) ... Setting up libxcb-render0:i386 (1.15-1) ... Setting up libboost-chrono-dev:i386 (1.74.0.3) ... Setting up libfftw3-bin (3.3.10-1) ... Setting up libwacom9:i386 (2.6.0-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libboost-math-dev:i386 (1.74.0.3) ... Setting up libxcb-glx0:i386 (1.15-1) ... Setting up libboost-coroutine1.74.0:i386 (1.74.0+ds1-21) ... Setting up libwebpdemux2:i386 (1.2.4-0.2+deb12u1) ... Setting up libedit2:i386 (3.1-20221030-2) ... Setting up libreadline8:i386 (8.2-1.3) ... Setting up libboost-system-dev:i386 (1.74.0.3) ... Setting up libpng-dev:i386 (1.6.39-2) ... Setting up libxcb-keysyms1:i386 (0.4.0-1+b2) ... Setting up libxcb-shape0:i386 (1.15-1) ... Setting up libavahi-common3:i386 (0.8-10) ... Setting up libjpeg-dev:i386 (1:2.1.5-2) ... Setting up libjbig-dev:i386 (2.1-6.1) ... Setting up libevent-openssl-2.1-7:i386 (2.1.12-stable-8) ... Setting up libxcb-render-util0:i386 (0.3.9-1+b1) ... Setting up libboost-tools-dev (1.74.0.3) ... Setting up libgfortran-12-dev:i386 (12.2.0-14) ... Setting up libxcb-shm0:i386 (1.15-1) ... Setting up libxcb-icccm4:i386 (0.4.1-1.1) ... Setting up libboost-nowide-dev (1.74.0.3) ... Setting up libldap-2.5-0:i386 (2.5.13+dfsg-5) ... Setting up libboost-container-dev:i386 (1.74.0.3) ... Setting up libxcb-util1:i386 (0.4.0-1+b1) ... Setting up pkgconf:i386 (1.8.1-1) ... Setting up libinput-bin (1.22.1-1) ... Setting up libxcb-xkb1:i386 (1.15-1) ... Setting up libxcb-image0:i386 (0.4.0-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:i386 (2.0.16-1) ... Setting up libnl-route-3-200:i386 (3.7.0-0.2+b1) ... Setting up libboost-test-dev:i386 (1.74.0.3) ... Setting up libxcb-present0:i386 (1.15-1) ... Setting up libcifpp5:i386 (5.0.7.1-1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:i386 (2.4.7-5) ... Setting up libxdmcp-dev:i386 (1:1.1.2-3) ... Setting up gfortran-12 (12.2.0-14) ... Setting up libwebp-dev:i386 (1.2.4-0.2+deb12u1) ... Setting up libxcb-xinerama0:i386 (1.15-1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:i386 (2.12.1+dfsg-5) ... Setting up libtiff-dev:i386 (4.5.0-6+deb12u1) ... Setting up libxcb-sync1:i386 (1.15-1) ... Setting up shared-mime-info (2.2-1) ... Setting up libxkbcommon-x11-0:i386 (1.5.0-1) ... Setting up libevent-dev (2.1.12-stable-8) ... Setting up libboost-random1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libeigen3-dev (3.4.0-4) ... Setting up libboost-timer1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libboost-numpy1.74-dev (1.74.0+ds1-21) ... Setting up pkg-config:i386 (1.8.1-1) ... Setting up libqt5core5a:i386 (5.15.8+dfsg-11) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up libboost-serialization1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libxcb-dri2-0:i386 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libboost-wave1.74.0:i386 (1.74.0+ds1-21) ... Setting up libdrm2:i386 (2.4.114-1+b1) ... Setting up dwz (0.15-1) ... Setting up libboost-regex1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libnl-3-dev:i386 (3.7.0-0.2+b1) ... Setting up libopenblas0:i386 (0.3.21+ds-4) ... Setting up groff-base (1.22.4-10) ... Setting up libqt5dbus5:i386 (5.15.8+dfsg-11) ... Setting up libxcb-randr0:i386 (1.15-1) ... Setting up libboost-stacktrace-dev:i386 (1.74.0.3) ... Setting up libllvm15:i386 (1:15.0.6-4+b1) ... Setting up libxslt1.1:i386 (1.1.35-1) ... Setting up libcurl4:i386 (7.88.1-10+deb12u4) ... Setting up libx11-6:i386 (2:1.8.4-2+deb12u2) ... Setting up libharfbuzz0b:i386 (6.0.0+dfsg-3) ... Setting up libhwloc-dev:i386 (2.9.0-1) ... Setting up libfontconfig1:i386 (2.14.1-4) ... Setting up libboost-locale1.74.0:i386 (1.74.0+ds1-21) ... Setting up libqt5test5:i386 (5.15.8+dfsg-11) ... Setting up libboost-regex-dev:i386 (1.74.0.3) ... Setting up libsm6:i386 (2:1.2.3-1) ... Setting up libfftw3-dev:i386 (3.3.10-1) ... Setting up libqt5concurrent5:i386 (5.15.8+dfsg-11) ... Setting up libavahi-client3:i386 (0.8-10) ... Setting up libboost-timer-dev:i386 (1.74.0.3) ... Setting up libboost-type-erasure1.74.0:i386 (1.74.0+ds1-21) ... Setting up liblbfgsb0:i386 (3.0+dfsg.4-1) ... Setting up libdrm-amdgpu1:i386 (2.4.114-1+b1) ... Setting up libopenblas-pthread-dev:i386 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/i386-linux-gnu/libblas.so (libblas.so-i386-linux-gnu) in auto mode update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/i386-linux-gnu/liblapack.so (liblapack.so-i386-linux-gnu) in auto mode update-alternatives: using /usr/lib/i386-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/i386-linux-gnu/libopenblas.so (libopenblas.so-i386-linux-gnu) in auto mode Setting up libxcb-dri3-0:i386 (1.15-1) ... Setting up libinput10:i386 (1.22.1-1) ... Setting up libx11-xcb1:i386 (2:1.8.4-2+deb12u2) ... Setting up libibverbs1:i386 (44.0-2) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:i386 (2.4.114-1+b1) ... Setting up libxcb1-dev:i386 (1.15-1) ... Setting up libboost-wave1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libxrender1:i386 (1:0.9.10-1.1) ... Setting up libgbm1:i386 (22.3.6-1+deb12u1) ... Setting up ibverbs-providers:i386 (44.0-2) ... Setting up libdrm-radeon1:i386 (2.4.114-1+b1) ... Setting up openssh-client (1:9.2p1-2+deb12u1) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:i386 (3.11.2-6) ... Setting up libdrm-intel1:i386 (2.4.114-1+b1) ... Setting up libgl1-mesa-dri:i386 (22.3.6-1+deb12u1) ... Setting up libx11-dev:i386 (2:1.8.4-2+deb12u2) ... Setting up libxext6:i386 (2:1.3.4-1+b1) ... Setting up libboost-random-dev:i386 (1.74.0.3) ... Setting up libboost-wave-dev:i386 (1.74.0.3) ... Setting up dssp (4.2.2-2) ... Setting up man-db (2.11.2-2) ... Not building database; man-db/auto-update is not 'true'. Setting up libqt5network5:i386 (5.15.8+dfsg-11) ... Setting up libxxf86vm1:i386 (1:1.1.4-1+b2) ... Setting up libxnvctrl0:i386 (525.85.05-3~deb12u1) ... Setting up libqt5sql5:i386 (5.15.8+dfsg-11) ... Setting up libboost-iostreams1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libnl-route-3-dev:i386 (3.7.0-0.2+b1) ... Setting up libboost-date-time1.74-dev:i386 (1.74.0+ds1-21) ... Setting up qtbase5-dev-tools (5.15.8+dfsg-11) ... Setting up libopenblas-dev:i386 (0.3.21+ds-4) ... Setting up libqt5xml5:i386 (5.15.8+dfsg-11) ... Setting up libegl-mesa0:i386 (22.3.6-1+deb12u1) ... Setting up libxfixes3:i386 (1:6.0.0-2) ... Setting up libboost-graph1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libraqm0:i386 (0.7.0-4.1) ... Setting up libboost-numpy-dev (1.74.0.3) ... Setting up libboost-serialization-dev:i386 (1.74.0.3) ... Setting up libboost-date-time-dev:i386 (1.74.0.3) ... Setting up libxext-dev:i386 (2:1.3.4-1+b1) ... Setting up libcups2:i386 (2.4.2-3+deb12u5) ... Setting up libegl1:i386 (1.6.0-1) ... Setting up cmake (3.25.1-1) ... Setting up libboost-thread1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libxss1:i386 (1:1.2.3-1) ... Setting up libboost-thread-dev:i386 (1.74.0.3) ... Setting up libpython3-stdlib:i386 (3.11.2-1+b1) ... Setting up librdmacm1:i386 (44.0-2) ... Setting up libboost-graph-dev:i386 (1.74.0.3) ... Setting up python3.11 (3.11.2-6) ... Setting up libxft2:i386 (2.3.6-1) ... Setting up libglx-mesa0:i386 (22.3.6-1+deb12u1) ... Setting up libboost-log1.74-dev (1.74.0+ds1-21) ... Setting up libpython3.11:i386 (3.11.2-6) ... Setting up libglx0:i386 (1.6.0-1) ... Setting up libtk8.6:i386 (8.6.13-2) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libboost-iostreams-dev:i386 (1.74.0.3) ... Setting up libibverbs-dev:i386 (44.0-2) ... Setting up libhwloc-plugins:i386 (2.9.0-1) ... Setting up libboost-context1.74-dev:i386 (1.74.0+ds1-21) ... Setting up python3-tz (2022.7.1-4) ... Setting up python3-six (1.16.0-4) ... Setting up libboost-fiber1.74-dev:i386 (1.74.0+ds1-21) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-packaging (23.0-1) ... Setting up libgl1:i386 (1.6.0-1) ... Setting up libboost-type-erasure1.74-dev:i386 (1.74.0+ds1-21) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up libpython3.11-dev:i386 (3.11.2-6) ... Setting up python3-brotli (1.0.9-2+b6) ... Setting up python3-cycler (0.11.0-1) ... Setting up python3-kiwisolver (1.4.4-1+b1) ... Setting up libboost-locale1.74-dev:i386 (1.74.0+ds1-21) ... Setting up python3-pyqt5.sip (12.11.1-1) ... Setting up python3-lxml:i386 (4.9.2-1+b1) ... Setting up libglx-dev:i386 (1.6.0-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up libboost-coroutine1.74-dev:i386 (1.74.0+ds1-21) ... Setting up libboost-coroutine-dev:i386 (1.74.0.3) ... Setting up python3-mpmath (1.2.1-2) ... Setting up python3-lib2to3 (3.11.2-3) ... Setting up python3-appdirs (1.4.4-3) ... Setting up libboost-log-dev (1.74.0.3) ... Setting up libgl-dev:i386 (1.6.0-1) ... Setting up libboost-fiber-dev:i386 (1.74.0.3) ... Setting up python3-pkg-resources (66.1.1-1) ... Setting up python3-distutils (3.11.2-3) ... Setting up dh-python (5.20230130+deb12u1) ... Setting up libfabric1:i386 (1.17.0-3) ... Setting up python3-sympy (1.11.1-1) ... Setting up python3-attr (22.2.0-1) ... Setting up tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Setting up libvulkan-dev:i386 (1.3.239.0-1) ... Setting up libpython3-dev:i386 (3.11.2-1+b1) ... Setting up libegl-dev:i386 (1.6.0-1) ... Setting up libpmix2:i386 (4.2.2-1+deb12u1) ... Setting up python3-lz4 (4.0.2+dfsg-1+b2) ... Setting up python3.11-dev (3.11.2-6) ... Setting up libopenmpi3:i386 (4.1.4-3+b1) ... Setting up blt (2.5.3+dfsg-4.1) ... Setting up python3-ply (3.11-5) ... Setting up libboost-mpi1.74.0 (1.74.0+ds1-21) ... Setting up libqt5gui5:i386 (5.15.8+dfsg-11) ... Setting up python3-gast (0.5.2-2) ... Setting up python3-all (3.11.2-1+b1) ... Setting up python3-tk:i386 (3.11.2-3) ... Setting up libboost-locale-dev:i386 (1.74.0.3) ... Setting up libqt5widgets5:i386 (5.15.8+dfsg-11) ... Setting up libboost-context-dev:i386 (1.74.0.3) ... Setting up libqt5help5:i386 (5.15.8-2) ... Setting up libboost-type-erasure-dev:i386 (1.74.0.3) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-beniget (0.4.1-3) ... Setting up libqt5printsupport5:i386 (5.15.8+dfsg-11) ... Setting up libpython3-all-dev:i386 (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up libglu1-mesa-dev:i386 (9.0.2-1.1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up qtbase5-dev:i386 (5.15.8+dfsg-11) ... Setting up libqt5opengl5:i386 (5.15.8+dfsg-11) ... Setting up python3-contourpy (1.0.7-1+b1) ... Setting up libboost-graph-parallel1.74.0 (1.74.0+ds1-21) ... Setting up libpmix-dev:i386 (4.2.2-1+deb12u1) ... Setting up openmpi-bin (4.1.4-3+b1) ... update-alternatives: using /usr/bin/mpirun.openmpi to provide /usr/bin/mpirun (mpirun) in auto mode update-alternatives: using /usr/bin/mpicc.openmpi to provide /usr/bin/mpicc (mpi) in auto mode Setting up python3-all-dev (3.11.2-1+b1) ... Setting up libqt5designer5:i386 (5.15.8-2) ... Setting up libqt5opengl5-dev:i386 (5.15.8+dfsg-11) ... Setting up mpi-default-bin (1.14) ... Setting up libboost-python1.74-dev (1.74.0+ds1-21) ... Setting up libboost-python-dev (1.74.0.3) ... Setting up libboost-graph-parallel1.74-dev (1.74.0+ds1-21) ... Setting up python3-pythran (0.11.0+ds-7) ... Setting up libopenmpi-dev:i386 (4.1.4-3+b1) ... update-alternatives: using /usr/lib/i386-linux-gnu/openmpi/include to provide /usr/include/i386-linux-gnu/mpi (mpi-i386-linux-gnu) in auto mode Setting up python3-pyqt5 (5.15.9+dfsg-1) ... Setting up libboost-mpi-python1.74.0 (1.74.0+ds1-21) ... Setting up python3-scipy (1.10.1-2) ... Setting up libboost-graph-parallel-dev (1.74.0.3) ... Setting up mpi-default-dev (1.14) ... Setting up libboost-mpi1.74-dev (1.74.0+ds1-21) ... Setting up libboost-mpi-python1.74-dev (1.74.0+ds1-21) ... Setting up libboost-mpi-python-dev (1.74.0.3) ... Setting up libboost-mpi-dev (1.74.0.3) ... Setting up libboost-all-dev (1.74.0.3) ... Setting up python3-fonttools (4.38.0-1+b1) ... Setting up python3-pil:i386 (9.4.0-1.1+b1) ... Setting up python3-pil.imagetk:i386 (9.4.0-1.1+b1) ... Setting up python3-ufolib2 (0.14.0+dfsg1-1) ... Setting up python3-matplotlib (3.6.3-1+b1) ... Processing triggers for libc-bin (2.36-9+deb12u3) ... 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: Running cd /build/reproducible-path/openstructure-2.3.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-genchanges -S > ../openstructure_2.3.1-9_source.changes dpkg-buildpackage: info: source package openstructure dpkg-buildpackage: info: source version 2.3.1-9 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Andrius Merkys dpkg-source --before-build . dpkg-buildpackage: info: host architecture i386 debian/rules clean dh clean --with python3 dh_clean debian/rules binary dh binary --with python3 dh_update_autotools_config dh_autoreconf debian/rules override_dh_auto_configure make[1]: Entering directory '/build/reproducible-path/openstructure-2.3.1' dh_auto_configure -- -DOPTIMIZE=ON -DUBUNTU_LAYOUT=ON cd obj-i686-linux-gnu && cmake -DCMAKE_INSTALL_PREFIX=/usr -DCMAKE_BUILD_TYPE=None -DCMAKE_INSTALL_SYSCONFDIR=/etc -DCMAKE_INSTALL_LOCALSTATEDIR=/var -DCMAKE_EXPORT_NO_PACKAGE_REGISTRY=ON -DCMAKE_FIND_USE_PACKAGE_REGISTRY=OFF -DCMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY=ON -DFETCHCONTENT_FULLY_DISCONNECTED=ON -DCMAKE_INSTALL_RUNSTATEDIR=/run -DCMAKE_SKIP_INSTALL_ALL_DEPENDENCY=ON "-GUnix Makefiles" -DCMAKE_VERBOSE_MAKEFILE=ON -DCMAKE_INSTALL_LIBDIR=lib/i386-linux-gnu -DOPTIMIZE=ON -DUBUNTU_LAYOUT=ON .. -- The CXX compiler identification is GNU 12.2.0 -- The C compiler identification is GNU 12.2.0 -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- Check for working CXX compiler: /usr/bin/c++ - skipped -- Detecting CXX compile features -- Detecting CXX compile features - done -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Check for working C compiler: /usr/bin/cc - skipped -- Detecting C compile features -- Detecting C compile features - done -- Looking for sys/types.h -- Looking for sys/types.h - found -- Looking for stdint.h -- Looking for stdint.h - found -- Looking for stddef.h -- Looking for stddef.h - found -- Check size of void* -- Check size of void* - done -- Found Python: /usr/bin/python3 (found suitable version "3.11.2", minimum required is "3.6") found components: Interpreter Development Development.Module Development.Embed -- Found Boost package: python311 -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.31") found components: unit_test_framework -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.31") found components: filesystem system -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.31") found components: iostreams regex -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.31") found components: program_options -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.31") found components: regex -- Performing Test CMAKE_HAVE_LIBC_PTHREAD -- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Success -- Found Threads: TRUE -- Found Boost: /usr/include (found suitable version "1.74.0", minimum required is "1.31") found components: thread chrono date_time atomic -- Found OpenGL: /usr/lib/i386-linux-gnu/libOpenGL.so -- Found EIGEN: /usr/include/eigen3 (Required is at least version "3.2.0") -- Found SQLITE3: /usr/lib/i386-linux-gnu/libsqlite3.so (Required is at least version "3.7.13") -- Found ZLIB: /usr/lib/i386-linux-gnu/libz.so (found version "1.2.13") -- Found PNG: /usr/lib/i386-linux-gnu/libpng.so (found version "1.6.39") -- Found FFTW: /usr/lib/i386-linux-gnu/libfftw3f.so -- Found TIFF: /usr/lib/i386-linux-gnu/libtiff.so (found version "4.5.0") -- Searching for python module PyQt5 for /usr/bin/python3 -- Found python module PyQt5 -- Searching for python module PyQt5.sip for /usr/bin/python3 -- Found python module PyQt5.sip -- OpenStructure will be built with the following options: Install Prefix (-DPREFIX) : /usr RPath in install (-DUSE_RPATH) : OFF Info support (-DENABLE_INFO) : ON Graphical interface (-DENABLE_GUI) : ON OpenGL support (-DENABLE_GFX) : ON Shader support (-DUSE_SHADER) : OFF Numpy support (-DUSE_NUMPY) : OFF SpaceNav Device support (-DENABLE_SPNAV) : OFF OpenMM support (-DENABLE_MM) : OFF OpenMM plugins (-DOPEN_MM_PLUGIN_DIR) : NONE Optimize (-DOPTIMIZE) : ON Profiling support (-DPROFILE) : OFF Double Precision (-DUSE_DOUBLE_PRECISION) : OFF Compound Lib (-DCOMPOUND_LIB) : NONE TMAlign and TMScore (-DCOMPILE_TMTOOLS) : OFF Static Libraries (-DENABLE_STATIC) : OFF Debian/Ubuntu directory layout (-DUBUNTU_LAYOUT) : ON Hidden object visibility (-DHIDDEN_VISIBILITY) : OFF -- Configuring done -- Generating done CMake Warning: Manually-specified variables were not used by the project: CMAKE_EXPORT_NO_PACKAGE_REGISTRY CMAKE_FIND_PACKAGE_NO_PACKAGE_REGISTRY CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_RUNSTATEDIR CMAKE_INSTALL_SYSCONFDIR FETCHCONTENT_FULLY_DISCONNECTED -- Build files have been written to: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu make[1]: Leaving directory '/build/reproducible-path/openstructure-2.3.1' dh_auto_build cd obj-i686-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/openstructure-2.3.1 -B/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/CMakeFiles /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/depend make -f modules/base/pymod/CMakeFiles/subst___init__.py.dir/build.make modules/base/pymod/CMakeFiles/subst___init__.py.dir/depend make -f modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build.make modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/depend make -f modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build.make modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src/CMakeFiles/create_stage.dir/DependInfo.cmake --color= make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod/CMakeFiles/subst___init__.py.dir/DependInfo.cmake --color= make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/DependInfo.cmake --color= make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/DependInfo.cmake --color= make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/db/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/pymod/CMakeFiles/ost_db_pymod.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gui/share /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share/CMakeFiles/scene_icons.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/base/pymod/CMakeFiles/subst___init__.py.dir/build.make modules/base/pymod/CMakeFiles/subst___init__.py.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.3.1/modules/base/pymod/__init__.py.in -DOUT_FILE=__init__.py -DALL_ADDITIONAL_MODULES=,\'gui\',\'gfx\',\'img\',\'info\' -P /build/reproducible-path/openstructure-2.3.1/cmake_support/substitute.cmake make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build.make modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build.make modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build make -f modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build.make modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./__init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./__init__.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/./__init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./__init__.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/db/pymod/./__init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/db/./__init__.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/./__init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/geom/./__init__.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/icons/add_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/icons/add_icon.png cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/./__init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./__init__.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/bin cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./lga.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./lga.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/./cleanup.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./cleanup.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/./py_gfx_obj.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./py_gfx_obj.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/icons/close_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/icons/close_icon.png cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/openstructure/libexec make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./hbplus.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hbplus.py [ 0%] Built target ost_geom_pymod [ 0%] Built target ost_db_pymod [ 0%] Built target subst___init__.py make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/depend make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/depend make -f modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/depend make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gui/share /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share/CMakeFiles/gui_images.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/icons/critical_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/icons/critical_icon.png cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/tests [ 0%] Built target ost_conop_pymod cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./msms.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./msms.py make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/depend [ 0%] Built target ost_gfx_pymod make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/__init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/__init__.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/icons/delete_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/icons/delete_icon.png make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/images/logo-small.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/images/logo-small.png make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./tmtools.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./tmtools.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/dng/__init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/__init__.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/color_options_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_options_widget.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/./__init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./__init__.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/icons/distance_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/icons/distance_icon.png make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build.make modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/./__init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/./__init__.py [ 0%] Built target create_stage make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build.make modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./dssp.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dssp.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/color_select_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_select_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/dng/termuse.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/termuse.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/./init_context_menu.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_context_menu.py [ 0%] Built target gui_images cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/icons/find_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/icons/find_icon.png make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/info/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/pymod/CMakeFiles/ost_info_pymod.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build.make modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/alg/./__init__.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/dng/superpositiondialog.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/superpositiondialog.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./clustalw.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./clustalw.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/combo_options_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/combo_options_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/./init_menubar.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_menubar.py [ 0%] Built target ost_img_pymod cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/icons/information_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/icons/information_icon.png make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/depend make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/io/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod/CMakeFiles/ost_io_pymod.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/pymod/./__init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/info/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/dng/init.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/init.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/./init_spacenav.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_spacenav.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/cpk_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/cpk_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./utils.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./utils.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/icons/map_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/icons/map_icon.png make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/./__init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 0%] Built target ost_img_alg_pymod make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/./init_splash.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_splash.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./naccess.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./naccess.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/custom_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/custom_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/dng/menu.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/menu.py [ 0%] Built target ost_info_pymod cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/icons/menubar_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/icons/menubar_icon.png make -f modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build.make modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/./remote.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./remote.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build.make modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/./__init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/./__init__.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/./trajectory_viewer.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./trajectory_viewer.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./hhblits.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/gradient_editor_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_editor_widget.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/icons/rigid_body_manipulator_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/icons/rigid_body_manipulator_icon.png make -f modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build.make modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/./repository.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./repository.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./__init__.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 0%] Built target ost_gui_dng_pymod cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./hhblits2.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits2.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/./helpwidget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./helpwidget.py make -f modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build.make modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/depend cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/gradient_info_handler.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_info_handler.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/icons/selection_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/icons/selection_icon.png cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/./views.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./views.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 0%] Built target ost_mol_pymod make -f modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build.make modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/depend cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/./table.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./table.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/gradient_list_model.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_list_model.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build.make modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./hhblits3.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits3.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/pymod/./__init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/./__init__.py [ 0%] Built target ost_io_pymod cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/icons/show_sidebar_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/icons/show_sidebar_icon.png make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/depend cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/./superpose.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./superpose.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts/CMakeFiles/subst_ost_startup.py.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/./gosty_startup.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./gosty_startup.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/gradient_preset_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_preset_widget.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./blast.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./blast.py make -f modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build.make modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod/./__init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./__init__.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/icons/site_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/icons/site_icon.png make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/./qsscoring.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./qsscoring.py make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.3.1/scripts/ost_startup.py.in -DOUT_FILE=ost_startup.py -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.3.1/cmake_support/substitute.cmake make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./cadscore.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./cadscore.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/hsc_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/hsc_widget.py [ 0%] Built target ost_seq_pymod cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod/./mat.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./mat.py make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts/CMakeFiles/subst_ost_config.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/icons/split_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/icons/split_icon.png cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/./trajectory_analysis.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./trajectory_analysis.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/immutable_gradient_info_handler.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_gradient_info_handler.py [ 0%] Built target ost_gui_pymod make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts/CMakeFiles/subst_ost.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod/./renumber.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./renumber.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./kclust.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./kclust.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.3.1/scripts/ost_config.in -DOUT_FILE=ost_config -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.3.1/cmake_support/substitute.cmake cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/icons/warning_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/icons/warning_icon.png cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/./structure_analysis.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./structure_analysis.py [ 0%] Built target subst_ost_startup.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/immutable_preset_info_handler.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_preset_info_handler.py make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts/CMakeFiles/subst_dng.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod/./aaindex.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./aaindex.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./ialign.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./ialign.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/share/icons/refresh.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/gui/icons/refresh.png make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.3.1/scripts/ost.in -DOUT_FILE=ost -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.3.1/cmake_support/substitute.cmake cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/./helix_kinks.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./helix_kinks.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/init_inspector.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/init_inspector.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.3.1/scripts/dng.in -DOUT_FILE=dng -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.3.1/cmake_support/substitute.cmake cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod/aaindex1 /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/aaindex/aaindex1 cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/./mmseqs2.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./mmseqs2.py [ 0%] Built target subst_ost_config make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/actions /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/actions /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/inspector_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/inspector_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/./hbond.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./hbond.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod/aaindex2 /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/aaindex/aaindex2 make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 0%] Built target subst_ost [ 0%] Built target scene_icons make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/actions/ost-compare-structures /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/openstructure/libexec/ost-compare-structures make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/geom/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src/CMakeFiles/ost_geom_headers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/config /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/config /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/config/CMakeFiles/ost_config_headers.dir/DependInfo.cmake --color= [ 0%] Built target subst_dng make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/map_level_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/map_level_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod/aaindex3 /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/aaindex/aaindex3 [ 0%] Built target ost_bindings_pymod make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/depend make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src/CMakeFiles/ost_base_headers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod/CMakeFiles/ost_base_pymod.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/export_helper/vector.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/export_helper/vector.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/config/./base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./base.hh [ 0%] Built target ost_mol_alg_pymod [ 0%] Built target actions make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/depend cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/preset.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/DependInfo.cmake --color= make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/depend make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/info/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src/CMakeFiles/ost_info_headers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/pymod/./settings.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/./settings.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./def.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./def.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/export_helper/generic_property_def.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/export_helper/generic_property_def.hh [ 0%] Built target ost_seq_alg_pymod cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/config/./config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./config.hh make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/depend make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/DependInfo.cmake --color= make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/remote.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/remote.py make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./exc.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./exc.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/export_helper/pair_to_tuple_conv.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/pymod/./stutil.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/preset_editor_list_model.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_list_model.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_error.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_error.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/pointer_iterator.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/config/./dllexport.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./dllexport.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/export_helper/vec_to_list_conv.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/export_helper/vec_to_list_conv.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/preset_editor_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/pymod/./table.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./geom.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./geom.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/config/./version.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./version.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/test_utils/compare_files.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/test_utils/compare_files.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/preset_info_handler.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_info_handler.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/atom_group.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/atom_group.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./mat.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./mat.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_handle.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./generic_property.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./generic_property.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/pymod/./table_selector.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table_selector.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/atom_prop.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/atom_prop.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/preset_list_model.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_list_model.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_iterator.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./mat2.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./mat2.hh [ 0%] Built target ost_config_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_group.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_group.hh make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/bindings/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/pymod/./xmlrunner.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./sequence_list.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./sequence_list.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/preset_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./mat3.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./mat3.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./integrity_error.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./integrity_error.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_item.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_item.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/src/./wrap_tmalign.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/bindings/./wrap_tmalign.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./sequence_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./sequence_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/pymod/./testutils.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/./testutils.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./mat4.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./mat4.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/render_mode_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_mode_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./invalid_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./invalid_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vec.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vec.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./alignment_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./alignment_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different __init__.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/__init__.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/render_op.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_op.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./ptr_observer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./ptr_observer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vec2.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vec2.hh [ 0%] Built target ost_bindings_headers make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/render_options_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_options_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_path.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_path.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/conop/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src/CMakeFiles/ost_conop_headers.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./sequence_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./sequence_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vec3.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vec3.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/scene_observer_impl.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_observer_impl.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./log.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./log.hh [ 0%] Built target ost_base_pymod cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_set.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_set.hh make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/db/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src/CMakeFiles/ost_db_headers.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./log_sink.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./log_sink.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/scene_selection_helper.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_selection_helper.py make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./aligned_region.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./aligned_region.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vec4.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vec4.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./conop.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./conop.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/dihedral.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_visitor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_visitor.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/db/src/./sqlite_wrap.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/./sqlite_wrap.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./profile.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./profile.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./aligned_column.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./aligned_column.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./processor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./processor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/simple_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/simple_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vecmat_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vecmat_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_verbose_visitor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_verbose_visitor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/db/src/./sqlite_conv.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/./sqlite_conv.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./amino_acids.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./amino_acids.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./dyn_cast.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./dyn_cast.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/sline_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/sline_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./aligned_column_iterator.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./aligned_column_iterator.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/entity_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vecmat2_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./item_type.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./item_type.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/db/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vecmat3_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./diag.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./diag.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./stdint.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./stdint.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./geom_info_conversion.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./geom_info_conversion.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/toolbar_options_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/toolbar_options_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./invalid_sequence.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./invalid_sequence.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/fragment_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/db/src/./linear_indexer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/./linear_indexer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./stdint_msc.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./stdint_msc.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vecmat4_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./model_check.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./model_check.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./item_type_cast.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./item_type_cast.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/fragment_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/trace_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/trace_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./views_from_sequences.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/db/src/./binary_container.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/./binary_container.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./circular_iterator.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./circular_iterator.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./range.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./range.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./profile_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./profile_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./heuristic.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./heuristic.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/query_ast.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/query_ast.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/tube_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/tube_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/db/src/./extract_data_helper.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/./extract_data_helper.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./compound.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./compound.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./constants.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./constants.hh [ 0%] Built target ost_info_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/query_ast_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/uniform_color_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/uniform_color_widget.py make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./module_config.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./composite.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./composite.hh [ 0%] Built target ost_seq_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./compound_lib.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./compound_lib.hh make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_headers.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/query_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/visibility_op.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/visibility_op.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./units.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./units.hh [ 0%] Built target ost_db_headers make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/depend make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./alignment_opts.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./alignment_opts.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./composite2.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./composite2.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./module_config.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/line_trace_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/line_trace_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/query_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/query_impl_fw.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./message.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./message.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./clip_alignment.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./composite3.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./composite3.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./anisotropic.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./anisotropic.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./rule_based.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./rule_based.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/wireframe_widget.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/wireframe_widget.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./platform.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./platform.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/dispatch.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/dispatch.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./conservation.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./conservation.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./auto_correlate.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./composite_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./composite_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./minimal_compound_lib.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/query_editor.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/query_editor.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/residue_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./contact_prediction_score.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./contact_prediction_score.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./string_ref.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./string_ref.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./clear.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./clear.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./composite2_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./composite2_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/surface_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./compound_lib_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_fw.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./contact_weight_matrix.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./clip_min_max.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./clip_min_max.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./pod_vector.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./pod_vector.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./composite3_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./composite3_op.hh [ 0%] Built target ost_gui_scene_pymod make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/depend cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/surface_impl_fw.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/io/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src/CMakeFiles/ost_io_headers.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./ring_finder.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./ring_finder.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./distance_map.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./distance_map.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./conjugate.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./conjugate.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./fixed_string.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./fixed_string.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./aligned_cuboid.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./aligned_cuboid.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_base_fw.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./tri_matrix.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./tri_matrix.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./entropy.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./entropy.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./convolute.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./convolute.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vec_mat_predicates.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vec_mat_predicates.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_def.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/star_parser.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/star_parser.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./quat.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./quat.hh [ 0%] Built target ost_conop_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./boost_filesystem_helper.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./global_align.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./global_align.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./correlate.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./correlate.hh make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./atom_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./atom_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_factory.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./transform.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./transform.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./ins_del.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./ins_del.hh make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./paged_array.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./paged_array.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./cross_correlate.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./cross_correlate.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./svd_superpose.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./svd_superpose.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./atom_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./atom_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_frequency_domain.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_frequency_domain.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/mmcif_info.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./point_cloud.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./point_cloud.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./density_slice.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./density_slice.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./local_align.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./local_align.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./atom_view.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./atom_view.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./module_config.hh [ 0%] Built target ost_base_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./merge_pairwise_alignments.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./merge_pairwise_alignments.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./dft.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./dft.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/io_profile.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/io_profile.hh make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gfx/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./sec_structure_segments.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./bond_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./bond_handle.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./local_dist_diff_test.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./local_dist_diff_test.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/dcd_io.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/dcd_io.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./fft.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./fft.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./module_config.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_spatial_domain.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./bond_table.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./bond_table.hh [ 0%] Built target ost_geom_headers make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gui/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/entity_io_crd_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./fftw_helper.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./fftw_helper.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./distance_test_common.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./distance_test_common.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./pair_subst_weight_matrix.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./pair_subst_weight_matrix.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_visitor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./chain_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./chain_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/entity_io_pqr_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./fill.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./fill.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./distance_rmsd_test.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./distance_rmsd_test.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./semiglobal_align.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./semiglobal_align.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_algorithm.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./chain_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./chain_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_option_group.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/entity_io_mae_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./filter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./filter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./superpose_frames.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./sequence_identity.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./sequence_identity.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./chain_view.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./chain_view.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_visitor_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_spec.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./filter_clashes.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./fourier_filters.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./sequence_similarity.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./sequence_similarity.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./chain_type.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./chain_type.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/index.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/index.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_bar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_octree.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/entity_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./chem_class.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./chem_class.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./construct_cbeta.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./gaussian_gradient_magnitude.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./gaussian_gradient_magnitude.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/selection_tool.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/type_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/type_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./subst_weight_matrix.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./subst_weight_matrix.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./clash_score.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./gaussian.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./gaussian.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./chem_type.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./chem_type.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/value_holder.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/value_holder.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./variance_map.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./trajectory_analysis.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./trajectory_analysis.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/entity_io_pdb_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./gaussian_laplacian.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./algorithm.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./algorithm.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./coord_group.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./coord_group.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_option.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_option.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/custom_renderer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./data/default_contact_weight_matrix.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./default_contact_weight_matrix.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./structure_analysis.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./structure_analysis.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./circle_mask.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./circle_mask.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_manager.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./highest_peak_search_3d.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./highest_peak_search_3d.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./coord_source.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./coord_source.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_writer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/pdb_writer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./data/default_pair_subst_weight_matrix.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/entity_io_sdf_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./composite_mask.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./composite_mask.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_options_widget.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_options_widget.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./in_mem_coord_source.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./in_mem_coord_source.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./histogram.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./histogram.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./pdbize.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./pdbize.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./data_algorithm.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./data_algorithm.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/sdf_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/sdf_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/manipulator.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/manipulator.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./coord_frame.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./coord_frame.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./hmm_pseudo_counts.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./line_iterator.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./line_iterator.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./adjacency_bitmap.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./adjacency_bitmap.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./data_observer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./data_observer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./editor_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./editor_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./local_sigma_threshold.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./local_sigma_threshold.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./hmm_score.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./data_types.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./data_types.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./editor_type_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./mask_image.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./mask_image.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/save_entity.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/save_entity.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./contact_overlap.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./data.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./data.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./mol.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./mol.hh [ 0%] Built target ost_seq_alg_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/map_tool.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/map_tool.hh make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/depend cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/load_entity.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/load_entity.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./negate.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./negate.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/config /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/config /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/config/CMakeFiles/ost_config.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/line_trace_renderer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./domain_find.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./debug.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./debug.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./normalizer_factory.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./normalizer_factory.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/surface_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Nothing to be done for 'modules/config/CMakeFiles/ost_config.dir/build'. make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./similarity_matrix.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./similarity_matrix.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/base_row.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./dllexport.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./dllexport.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_base.hh [ 0%] Built target ost_config cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/load_surface.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/load_surface.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./norm.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./norm.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/background_painter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./extent_iterator.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./extent_iterator.hh make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/depend cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/geom/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src/CMakeFiles/ost_geom.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./accessibility.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./accessibility.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/surface_io_msms_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./normalizer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./normalizer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./extent_mask.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./extent_mask.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/conservation_painter.hh make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./sec_struct.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./sec_struct.hh make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_observer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_observer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./nonstandard.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./nonstandard.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_str.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/pdb_str.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./extent.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./extent.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./norm_linear.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./norm_linear.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat2.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/painter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/mat2.cc.o -MF CMakeFiles/ost_geom.dir/mat2.cc.o.d -o CMakeFiles/ost_geom.dir/mat2.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/src/mat2.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_observer_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./molck.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./molck.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image_factory.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image_factory.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./norm_log.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./norm_log.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_property_mapper.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/secstr_row.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./find_membrane.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./find_membrane.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./norm_od.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./norm_od.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/omf.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/omf.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_secstr_painter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_view.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_view.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/entity_renderer_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image_handle_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image_handle_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./entity_to_density.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./power_spectrum.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./power_spectrum.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_selection_painter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/load_map.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/load_map.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_visitor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_visitor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/tabulated_trig.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/tabulated_trig.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./randomize.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./randomize.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image_handle.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_text_painter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_visitor_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh [ 0%] Built target ost_mol_alg_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/fast_spheres.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./smooth_mask_image.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./smooth_mask_image.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./handle_type_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./handle_type_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_delegate.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat3.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/image_format.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/image_format.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image_list.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image_list.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/mat3.cc.o -MF CMakeFiles/ost_geom.dir/mat3.cc.o.d -o CMakeFiles/ost_geom.dir/mat3.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/src/mat3.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./stat.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./stat.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./ics_editor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./ics_editor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_model.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image_state_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image_state_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/line_render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_dx_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./stat_accumulator.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./stat_accumulator.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_row.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./not_connected_error.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./not_connected_error.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image_state.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image_state.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/custom_render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/custom_render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_spi_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./stat_min_max.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./stat_min_max.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_search_bar.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./property_id.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./property_id.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/cpk_render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/cpk_render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_situs_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./threshold.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./threshold.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./query.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./query.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_table_view.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/simple_render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./transcendentals.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./transcendentals.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./query_error.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./query_error.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./inverted_mask.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./inverted_mask.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/sline_render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/sline_render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_mrc_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./transform.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./transform.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./map.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./map.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/tick_painter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./query_state.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./query_state.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/line_trace_render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_dat_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./transform_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./transform_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./mask_base_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./mask_base_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/title_row.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./residue_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./residue_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/cartoon_render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/cartoon_render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./alg_transform.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./alg_transform.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_ipl_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/alignment_view_object.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./residue_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./residue_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./mask_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./mask_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/trace_render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./alg_mirror.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./alg_mirror.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./mask_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./mask_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./residue_prop.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./residue_prop.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_jpk_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/base_view_object.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_view_object.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./residue_view.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./residue_view.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./alg_shift.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./alg_shift.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_nanoscope_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./mask_visitor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./mask_visitor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/main_thread_runner.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./discrete_shrink.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./discrete_shrink.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./sec_structure.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./sec_structure.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_png_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./mask.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./mask.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./transformation_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./spatial_organizer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./spatial_organizer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./transformations.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./transformations.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./surface.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./surface.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/completer_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/completer_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/uniform_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./normalizer_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./normalizer_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./fractional_shift.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./fractional_shift.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/dir_model.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./surface_builder.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./surface_builder.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/tiff_util.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./normalizer_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./normalizer_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/entity_view_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./builder.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./builder.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/jpk_util.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/jpk_util.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/gutter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/gutter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./surface_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./surface_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./polar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./polar.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./null_data.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./null_data.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/basic_gradient_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/path_completer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/path_completer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./observable.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./observable.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./surface_prop.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./surface_prop.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./line_average.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./line_average.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/fasta_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_context_parser.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_context_parser.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./paste_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./paste_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./torsion_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./torsion_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./rscrosscorr.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./rscrosscorr.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_completer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_completer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/map_handle_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./peak.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./peak.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./transfer_connectivity.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./transfer_connectivity.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_shell.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./phase.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./phase.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./query_view_wrapper.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./query_view_wrapper.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./render_pass.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./render_pass.hh [ 0%] Built target ost_img_alg_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_shell_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/profile_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./physical_units.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./physical_units.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./view_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./bitmap_io.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat4.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_shell_widget.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/mat4.cc.o -MF CMakeFiles/ost_geom.dir/mat4.cc.o.d -o CMakeFiles/ost_geom.dir/mat4.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/src/mat4.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/hhm_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/hhm_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./pixel_sampling.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./pixel_sampling.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./view_type_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./view_type_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./collada_exporter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_tokenizer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_tokenizer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./point_list.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./point_list.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./view_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./color.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./color.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/pssm_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/pssm_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_syntax_highlighter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_syntax_highlighter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./xcs_editor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./xcs_editor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./point.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./point.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./entity.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./entity.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./bounding_box.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./bounding_box.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./polygon_mask.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./polygon_mask.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./entity_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./entity_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/load.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/load.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./transform.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./transform.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./progress.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./progress.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gl_helper.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gl_helper.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/save.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/save.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./size.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./size.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./binary_data_sink.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./binary_data_sink.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./spherical_mask.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./spherical_mask.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_text_document_layout.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_shell_text_document_layout.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_fw.hh [ 0%] Built target ost_mol_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./io_manager.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./io_manager.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./binary_data_source.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./binary_data_source.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./util.cc /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./util.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/shell_history.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/shell_history.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vec3.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vec3.cc.o -MF CMakeFiles/ost_geom.dir/vec3.cc.o.d -o CMakeFiles/ost_geom.dir/vec3.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/src/vec3.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./util.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./util.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_node_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/state_machine.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/state_machine.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_node_visitor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/state.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/state.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./container_serialization.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./container_serialization.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./value_util.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./value_util.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_object_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_object_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/transition.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/transition.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./swap_util.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./swap_util.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./vecmat.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./vecmat.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/transition_guard.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_object.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_object.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./io_utils.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./io_utils.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./mask_info_convert.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./mask_info_convert.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/button_bar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/button_bar.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_object_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_object_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./io_exception.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./io_exception.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_prim.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_prim.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/drop_box.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/drop_box.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./convert.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./convert.hh [ 0%] Built target ost_img_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./symmetry_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./symmetry_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/panel_bar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/panel_bar.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat2_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat2_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat2_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat2_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/src/vecmat2_op.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./converting_streams.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./converting_streams.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_test_object.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_test_object.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/panel_manager.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/panel_manager.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./formatted_line.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./formatted_line.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./glwin_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./glwin_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/bottom_bar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/bottom_bar.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/chemdict_parser.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./chemdict_parser.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./input.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./input.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/star_parser.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./star_parser.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/button_box.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/button_box.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./prim_list.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./prim_list.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/mmcif_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./mmcif_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/event_button.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/event_button.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./scene.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./scene.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/mmcif_info.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./mmcif_info.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/panel_widget_container.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/panel_widget_container.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./selection.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./selection.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/io_profile.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./io_profile.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/panel_bar_widget_holder.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/panel_bar_widget_holder.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./surface.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./surface.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/dcd_io.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./dcd_io.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/side_bar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/side_bar.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./texture.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./texture.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/entity_io_crd_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./entity_io_crd_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/splitter_panel_bar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/splitter_panel_bar.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./vertex_array.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./vertex_array.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/entity_io_pqr_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/tabbed_panel_bar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/tabbed_panel_bar.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./vertex_array_helper.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/entity_io_mae_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/context_menu.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./scene_observer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./scene_observer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/entity_io_mmcif_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gl_include.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gl_include.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/current_selection_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/entity_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./entity_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./glext_include.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./glext_include.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/custom_part_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/pdb_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./pdb_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./render_mode.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./render_mode.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/entity_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/entity_io_pdb_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./entity_io_pdb_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./material.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./material.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/entity_part_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/pdb_writer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./pdb_writer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gradient.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gradient.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/gfx_scene_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/entity_io_sdf_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gradient_manager.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gradient_manager.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/sdf_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./sdf_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/label_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/label_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/sdf_writer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./sdf_writer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/root_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/root_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./primitives.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./primitives.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/save_entity.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./save_entity.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./povray_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./povray_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/render_mode_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/load_entity.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./load_entity.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./povray.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./povray.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/render_modes_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/surface_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./surface_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./exporter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./exporter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/load_surface.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./load_surface.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./exporter_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./exporter_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/surface_io_msms_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gost_exporter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gost_exporter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./color_ops/map_handle_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./map_handle_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/pdb_str.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./pdb_str.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/messages/message_widget.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/messages/message_widget.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./map_iso.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./map_iso.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/messages/message_box_widget.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/stereochemical_params_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/messages/log_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/messages/log_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./map_slab.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./map_slab.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/omf.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./omf.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/argand.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/argand.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./map_iso_prop.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./map_iso_prop.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/sequence_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/fasta_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel.hh [ 0%] Built target ost_gfx_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/pir_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./pir_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel_base.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat3_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat3_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat3_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat3_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/src/vecmat3_op.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/promod_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./promod_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/draw_overlay.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/profile_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./profile_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/drawing_functions.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/hhm_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./hhm_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/fft_panel.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/pssm_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./pssm_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/info_panel.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/clustal_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./clustal_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/img2qt.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/load.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./load.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/mask_overlay.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/save.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./save.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/null_overlay.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/null_overlay.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/load_map.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./load_map.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/overlay.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_df3_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_df3_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/image_format.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./image_format.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_dx_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_dx_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_spi_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_spi_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_situs_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_situs_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_gui.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_gui.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_mrc_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_mrc_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_observer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_observer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_dat_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_dat_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_ipl_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_ipl_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_jpk_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_jpk_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/strategies.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_nanoscope_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_nanoscope_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/strategies_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/strategies_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/viewer_normalizer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_png_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_png_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./file_browser.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./file_browser.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_dm3_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_dm3_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_tiff_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_tiff_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./file_type_dialog.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./file_type_dialog.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/tiff_util.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./tiff_util.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./file_viewer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./file_viewer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/jpk_util.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./jpk_util.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./gl_canvas.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./gl_canvas.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./gl_win.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./gl_win.hh [ 0%] Built target ost_io_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./scene_menu.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./scene_menu.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./gosty_app.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./gosty_app.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat4_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/vecmat4_op.cc.o -MF CMakeFiles/ost_geom.dir/vecmat4_op.cc.o.d -o CMakeFiles/ost_geom.dir/vecmat4_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/src/vecmat4_op.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./admin.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./admin.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./main.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./main.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./main_area.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./main_area.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./perspective.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./perspective.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./scene_selection.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./scene_selection.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./main_window.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./main_window.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./dock_widget.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./dock_widget.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./dock_widget.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./dock_widget.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./thin_splitter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./thin_splitter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./widget.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./widget.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./widget_geom_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./widget_geom_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./widget_pool.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./widget_pool.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./widget_registry.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./widget_registry.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./widget_state_saver.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./widget_state_saver.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./file_loader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./file_loader.hh make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 0%] Built target ost_gui_headers [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite2.cc.o -MF CMakeFiles/ost_geom.dir/composite2.cc.o.d -o CMakeFiles/ost_geom.dir/composite2.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/src/composite2.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite3.cc.o -MF CMakeFiles/ost_geom.dir/composite3.cc.o.d -o CMakeFiles/ost_geom.dir/composite3.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/src/composite3.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite2_op.cc.o -MF CMakeFiles/ost_geom.dir/composite2_op.cc.o.d -o CMakeFiles/ost_geom.dir/composite2_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/src/composite2_op.cc In file included from /build/reproducible-path/openstructure-2.3.1/modules/geom/src/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/geom/src/composite2.cc:23: /build/reproducible-path/openstructure-2.3.1/modules/geom/src/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/geom/src/def.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/geom/src/composite2.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/geom/src/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/composite3_op.cc.o -MF CMakeFiles/ost_geom.dir/composite3_op.cc.o.d -o CMakeFiles/ost_geom.dir/composite3_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/src/composite3_op.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/quat.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/quat.cc.o -MF CMakeFiles/ost_geom.dir/quat.cc.o.d -o CMakeFiles/ost_geom.dir/quat.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/src/quat.cc In file included from /build/reproducible-path/openstructure-2.3.1/modules/geom/src/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/geom/src/composite2_op.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/geom/src/composite2_op.cc:24: /build/reproducible-path/openstructure-2.3.1/modules/geom/src/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/geom/src/composite2_op.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/geom/src/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/transform.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/transform.cc.o -MF CMakeFiles/ost_geom.dir/transform.cc.o.d -o CMakeFiles/ost_geom.dir/transform.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/src/transform.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -MF CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o.d -o CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/src/aligned_cuboid.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/point_cloud.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/src/CMakeFiles/ost_geom.dir/point_cloud.cc.o -MF CMakeFiles/ost_geom.dir/point_cloud.cc.o.d -o CMakeFiles/ost_geom.dir/point_cloud.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/src/point_cloud.cc [ 1%] Linking CXX shared library ../../../stage/lib/libost_geom.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_geom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_geom.so.2.3 -o ../../../stage/lib/libost_geom.so.2.3.1 CMakeFiles/ost_geom.dir/mat2.cc.o CMakeFiles/ost_geom.dir/mat3.cc.o CMakeFiles/ost_geom.dir/mat4.cc.o CMakeFiles/ost_geom.dir/vec3.cc.o CMakeFiles/ost_geom.dir/vecmat2_op.cc.o CMakeFiles/ost_geom.dir/vecmat3_op.cc.o CMakeFiles/ost_geom.dir/vecmat4_op.cc.o CMakeFiles/ost_geom.dir/composite2.cc.o CMakeFiles/ost_geom.dir/composite3.cc.o CMakeFiles/ost_geom.dir/composite2_op.cc.o CMakeFiles/ost_geom.dir/composite3_op.cc.o CMakeFiles/ost_geom.dir/quat.cc.o CMakeFiles/ost_geom.dir/transform.cc.o CMakeFiles/ost_geom.dir/aligned_cuboid.cc.o CMakeFiles/ost_geom.dir/point_cloud.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_geom.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3 ../../../stage/lib/libost_geom.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 1%] Built target ost_geom make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/depend make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src/CMakeFiles/ost_base.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod/CMakeFiles/_ost_geom.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/build make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 1%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/generic_property.cc.o [ 1%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec2.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/generic_property.cc.o -MF CMakeFiles/ost_base.dir/generic_property.cc.o.d -o CMakeFiles/ost_base.dir/generic_property.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/src/generic_property.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec2.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec2.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vec2.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/log.cc.o [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/log_sink.cc.o [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec3.cc.o [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/profile.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/log.cc.o -MF CMakeFiles/ost_base.dir/log.cc.o.d -o CMakeFiles/ost_base.dir/log.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/src/log.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vecmat3_op.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/log_sink.cc.o -MF CMakeFiles/ost_base.dir/log_sink.cc.o.d -o CMakeFiles/ost_base.dir/log_sink.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/src/log_sink.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/profile.cc.o -MF CMakeFiles/ost_base.dir/profile.cc.o.d -o CMakeFiles/ost_base.dir/profile.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/src/profile.cc [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec3.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec3.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vec3.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vecmat2_op.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/units.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/units.cc.o -MF CMakeFiles/ost_base.dir/units.cc.o.d -o CMakeFiles/ost_base.dir/units.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/src/units.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/string_ref.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/string_ref.cc.o -MF CMakeFiles/ost_base.dir/string_ref.cc.o.d -o CMakeFiles/ost_base.dir/string_ref.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/src/string_ref.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/platform.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/platform.cc.o -MF CMakeFiles/ost_base.dir/platform.cc.o.d -o CMakeFiles/ost_base.dir/platform.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/src/platform.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/message.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/message.cc.o -MF CMakeFiles/ost_base.dir/message.cc.o.d -o CMakeFiles/ost_base.dir/message.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/src/message.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o -MF CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o.d -o CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/src/test_utils/compare_files.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/src/CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -MF CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o.d -o CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/src/boost_filesystem_helper.cc [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec4.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec4.cc.o -MF CMakeFiles/_ost_geom.dir/export_vec4.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vec4.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vec4.cc [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vecmat4_op.cc [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/wrap_geom.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/wrap_geom.cc.o -MF CMakeFiles/_ost_geom.dir/wrap_geom.cc.o.d -o CMakeFiles/_ost_geom.dir/wrap_geom.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/wrap_geom.cc [ 2%] Linking CXX shared library ../../../stage/lib/libost_base.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_base.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_base.so.2.3 -o ../../../stage/lib/libost_base.so.2.3.1 CMakeFiles/ost_base.dir/generic_property.cc.o CMakeFiles/ost_base.dir/log.cc.o CMakeFiles/ost_base.dir/log_sink.cc.o CMakeFiles/ost_base.dir/profile.cc.o CMakeFiles/ost_base.dir/units.cc.o CMakeFiles/ost_base.dir/string_ref.cc.o CMakeFiles/ost_base.dir/platform.cc.o CMakeFiles/ost_base.dir/message.cc.o CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_base.so.2.3 ../../../stage/lib/libost_base.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 2%] Built target ost_base make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/info/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src/CMakeFiles/ost_info.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 2%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_impl.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_impl.cc.o -MF CMakeFiles/ost_info.dir/info_impl.cc.o.d -o CMakeFiles/ost_info.dir/info_impl.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_impl.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vec3.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vecmat2_op.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vec2.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vecmat3_op.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vec3.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vec2.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vecmat2_op.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vecmat3_op.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vec4.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vec4.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat2.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat2.cc.o -MF CMakeFiles/_ost_geom.dir/export_mat2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_mat2.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_mat2.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_impl.cc:37: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_impl.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vecmat4_op.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/wrap_geom.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_vecmat4_op.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/wrap_geom.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat3.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat3.cc.o -MF CMakeFiles/_ost_geom.dir/export_mat3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_mat3.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_mat3.cc [ 2%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat4.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat4.cc.o -MF CMakeFiles/_ost_geom.dir/export_mat4.cc.o.d -o CMakeFiles/_ost_geom.dir/export_mat4.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_mat4.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite2.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite2.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_composite2.cc [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite3.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite3.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_composite3.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_mat2.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_mat2.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_composite2_op.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_mat3.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_mat3.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_composite3.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_mat4.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_composite2.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 3%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -MF CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o.d -o CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_composite3_op.cc [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_handle.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_handle.cc.o -MF CMakeFiles/ost_info.dir/info_handle.cc.o.d -o CMakeFiles/ost_info.dir/info_handle.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_handle.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_mat4.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_composite2.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.cc.o -MF CMakeFiles/_ost_geom.dir/export_quat.cc.o.d -o CMakeFiles/_ost_geom.dir/export_quat.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_quat.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_composite3.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_composite2_op.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_composite2_op.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_group.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_handle.cc:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_handle.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_composite3_op.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.cc.o -MF CMakeFiles/_ost_geom.dir/export_transform.cc.o.d -o CMakeFiles/_ost_geom.dir/export_transform.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_transform.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_composite3_op.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_group.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_group.cc.o -MF CMakeFiles/ost_info.dir/info_group.cc.o.d -o CMakeFiles/ost_info.dir/info_group.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_group.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_quat.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_item.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_item.cc.o -MF CMakeFiles/ost_info.dir/info_item.cc.o.d -o CMakeFiles/ost_info.dir/info_item.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_item.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_quat.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_path.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_path.cc.o -MF CMakeFiles/ost_info.dir/info_path.cc.o.d -o CMakeFiles/ost_info.dir/info_path.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_path.cc [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_set.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_set.cc.o -MF CMakeFiles/ost_info.dir/info_set.cc.o.d -o CMakeFiles/ost_info.dir/info_set.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_set.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_group.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_group.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_handle.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/export_transform.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_group.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_item.cc:31: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_item.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_visitor.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_visitor.cc.o -MF CMakeFiles/ost_info.dir/info_visitor.cc.o.d -o CMakeFiles/ost_info.dir/info_visitor.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_visitor.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_group.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_set.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_set.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_set.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -MF CMakeFiles/ost_info.dir/geom_info_conversion.cc.o.d -o CMakeFiles/ost_info.dir/geom_info_conversion.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/info/src/geom_info_conversion.cc [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/c++ -DOST_MODULE_OST_INFO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_info_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -MF CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o.d -o CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_verbose_visitor.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/geom_info_conversion.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info_handle.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_group.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_verbose_visitor.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/info/src/info_verbose_visitor.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 5%] Linking CXX shared library ../../../stage/lib/libost_info.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_info.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_info.so.2.3 -o ../../../stage/lib/libost_info.so.2.3.1 CMakeFiles/ost_info.dir/info_impl.cc.o CMakeFiles/ost_info.dir/info_handle.cc.o CMakeFiles/ost_info.dir/info_group.cc.o CMakeFiles/ost_info.dir/info_item.cc.o CMakeFiles/ost_info.dir/info_path.cc.o CMakeFiles/ost_info.dir/info_set.cc.o CMakeFiles/ost_info.dir/info_visitor.cc.o CMakeFiles/ost_info.dir/geom_info_conversion.cc.o CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so [ 5%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/geom/_ost_geom.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_geom.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/geom/_ost_geom.so CMakeFiles/_ost_geom.dir/export_vec2.cc.o CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o CMakeFiles/_ost_geom.dir/export_vec3.cc.o CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o CMakeFiles/_ost_geom.dir/export_vec4.cc.o CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o CMakeFiles/_ost_geom.dir/wrap_geom.cc.o CMakeFiles/_ost_geom.dir/export_mat2.cc.o CMakeFiles/_ost_geom.dir/export_mat3.cc.o CMakeFiles/_ost_geom.dir/export_mat4.cc.o CMakeFiles/_ost_geom.dir/export_composite2.cc.o CMakeFiles/_ost_geom.dir/export_composite3.cc.o CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o CMakeFiles/_ost_geom.dir/export_quat.cc.o CMakeFiles/_ost_geom.dir/export_transform.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_info.so.2.3 ../../../stage/lib/libost_info.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 5%] Built target ost_info make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/depend make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src/CMakeFiles/ost_img.dir/DependInfo.cmake --color= [ 5%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o [ 5%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o [ 5%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o [ 5%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o [ 5%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o [ 5%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o -MF CMakeFiles/ost_mol.dir/atom_handle.cc.o.d -o CMakeFiles/ost_mol.dir/atom_handle.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/atom_handle.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o -MF CMakeFiles/ost_mol.dir/bond_handle.cc.o.d -o CMakeFiles/ost_mol.dir/bond_handle.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/bond_handle.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o -MF CMakeFiles/ost_mol.dir/atom_base.cc.o.d -o CMakeFiles/ost_mol.dir/atom_base.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/atom_base.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o -MF CMakeFiles/ost_mol.dir/atom_view.cc.o.d -o CMakeFiles/ost_mol.dir/atom_view.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/atom_view.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o -MF CMakeFiles/ost_mol.dir/chain_base.cc.o.d -o CMakeFiles/ost_mol.dir/chain_base.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/chain_base.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o -MF CMakeFiles/ost_mol.dir/chain_handle.cc.o.d -o CMakeFiles/ost_mol.dir/chain_handle.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/chain_handle.cc make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 5%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/circle_mask.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/circle_mask.cc.o -MF CMakeFiles/ost_img.dir/circle_mask.cc.o.d -o CMakeFiles/ost_img.dir/circle_mask.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/circle_mask.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/geom/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/geom/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 5%] Built target _ost_geom [ 5%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o -MF CMakeFiles/ost_mol.dir/chain_view.cc.o.d -o CMakeFiles/ost_mol.dir/chain_view.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/chain_view.cc In file included from /usr/include/boost/bind.hpp:30, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/chain_view.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/circle_mask.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/circle_mask.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/chain_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/chain_handle.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/chain_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/chain_base.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/chain_base.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/chain_base.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/atom_handle.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/atom_handle.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/atom_handle.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/atom_view.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/atom_view.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/atom_view.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/bond_handle.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/list:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/bond_handle.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/bond_handle.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/atom_base.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/atom_base.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/atom_base.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/chain_handle.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 5%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/composite_mask.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/composite_mask.cc.o -MF CMakeFiles/ost_img.dir/composite_mask.cc.o.d -o CMakeFiles/ost_img.dir/composite_mask.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/composite_mask.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/chain_view.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/algorithm:60, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/chain_view.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o -MF CMakeFiles/ost_mol.dir/chain_type.cc.o.d -o CMakeFiles/ost_mol.dir/chain_type.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/chain_type.cc [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_frame.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_frame.cc.o -MF CMakeFiles/ost_mol.dir/coord_frame.cc.o.d -o CMakeFiles/ost_mol.dir/coord_frame.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/coord_frame.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/composite_mask.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/composite_mask.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_group.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_group.cc.o -MF CMakeFiles/ost_mol.dir/coord_group.cc.o.d -o CMakeFiles/ost_mol.dir/coord_group.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/coord_group.cc [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/editor_base.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/editor_base.cc.o -MF CMakeFiles/ost_mol.dir/editor_base.cc.o.d -o CMakeFiles/ost_mol.dir/editor_base.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/editor_base.cc [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_base.cc.o -MF CMakeFiles/ost_mol.dir/entity_base.cc.o.d -o CMakeFiles/ost_mol.dir/entity_base.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_base.cc [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_handle.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_handle.cc.o -MF CMakeFiles/ost_mol.dir/entity_handle.cc.o.d -o CMakeFiles/ost_mol.dir/entity_handle.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_handle.cc [ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_algorithm.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data_algorithm.cc.o -MF CMakeFiles/ost_img.dir/data_algorithm.cc.o.d -o CMakeFiles/ost_img.dir/data_algorithm.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/data_algorithm.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/coord_group.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/coord_group.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/in_mem_coord_source.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/coord_frame.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/coord_frame.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 6%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.cc.o -MF CMakeFiles/ost_img.dir/data_observer.cc.o.d -o CMakeFiles/ost_img.dir/data_observer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/data_observer.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/editor_base.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/editor_base.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/editor_base.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/editor_base.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_base.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_base.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_base.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o -MF CMakeFiles/ost_mol.dir/entity_observer.cc.o.d -o CMakeFiles/ost_mol.dir/entity_observer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_observer.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_handle.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_handle.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_handle.hh:38, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/data_observer.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/data_observer.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/data_observer.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -MF CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o.d -o CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.cc [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o -MF CMakeFiles/ost_mol.dir/entity_view.cc.o.d -o CMakeFiles/ost_mol.dir/entity_view.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_view.cc [ 6%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_visitor.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_visitor.cc.o -MF CMakeFiles/ost_mol.dir/entity_visitor.cc.o.d -o CMakeFiles/ost_mol.dir/entity_visitor.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_visitor.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/ics_editor.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/ics_editor.cc.o -MF CMakeFiles/ost_mol.dir/ics_editor.cc.o.d -o CMakeFiles/ost_mol.dir/ics_editor.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/ics_editor.cc [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/data.cc.o -MF CMakeFiles/ost_img.dir/data.cc.o.d -o CMakeFiles/ost_img.dir/data.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/data.cc In file included from /usr/include/boost/bind.hpp:30, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/not_connected_error.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/not_connected_error.cc.o -MF CMakeFiles/ost_mol.dir/not_connected_error.cc.o.d -o CMakeFiles/ost_mol.dir/not_connected_error.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/not_connected_error.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o -MF CMakeFiles/ost_mol.dir/property_id.cc.o.d -o CMakeFiles/ost_mol.dir/property_id.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/property_id.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query.cc.o -MF CMakeFiles/ost_mol.dir/query.cc.o.d -o CMakeFiles/ost_mol.dir/query.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/query.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.hh:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/algorithm:60, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:40: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/data.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/data.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o -MF CMakeFiles/ost_mol.dir/query_error.cc.o.d -o CMakeFiles/ost_mol.dir/query_error.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/query_error.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/ics_editor.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/ics_editor.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/ics_editor.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/ics_editor.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o -MF CMakeFiles/ost_mol.dir/query_state.cc.o.d -o CMakeFiles/ost_mol.dir/query_state.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/query_state.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/query.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/query.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_iterator.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent_iterator.cc.o -MF CMakeFiles/ost_img.dir/extent_iterator.cc.o.d -o CMakeFiles/ost_img.dir/extent_iterator.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/extent_iterator.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o -MF CMakeFiles/ost_mol.dir/residue_base.cc.o.d -o CMakeFiles/ost_mol.dir/residue_base.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/residue_base.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o -MF CMakeFiles/ost_mol.dir/residue_handle.cc.o.d -o CMakeFiles/ost_mol.dir/residue_handle.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/residue_handle.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_view.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_view.cc.o -MF CMakeFiles/ost_mol.dir/residue_view.cc.o.d -o CMakeFiles/ost_mol.dir/residue_view.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/residue_view.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/extent_iterator.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/extent_iterator.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_builder.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_builder.cc.o -MF CMakeFiles/ost_mol.dir/surface_builder.cc.o.d -o CMakeFiles/ost_mol.dir/surface_builder.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/surface_builder.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/query_state.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/query_state.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/residue_view.cc:22: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/residue_base.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/residue_base.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_mask.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent_mask.cc.o -MF CMakeFiles/ost_img.dir/extent_mask.cc.o.d -o CMakeFiles/ost_img.dir/extent_mask.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/extent_mask.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_handle.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_handle.cc.o -MF CMakeFiles/ost_mol.dir/surface_handle.cc.o.d -o CMakeFiles/ost_mol.dir/surface_handle.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/surface_handle.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/residue_handle.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/residue_handle.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/residue_view.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/algorithm:60, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/residue_view.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/extent_mask.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/extent_mask.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/extent.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/surface_handle.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/surface_builder.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/surface_builder.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/surface_builder.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -MF CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o.d -o CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/surface_handle.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/surface_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/extent.cc.o -MF CMakeFiles/ost_img.dir/extent.cc.o.d -o CMakeFiles/ost_img.dir/extent.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/extent.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o -MF CMakeFiles/ost_mol.dir/torsion_handle.cc.o.d -o CMakeFiles/ost_mol.dir/torsion_handle.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/torsion_handle.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -MF CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o.d -o CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/query_view_wrapper.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/view_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/view_op.cc.o -MF CMakeFiles/ost_mol.dir/view_op.cc.o.d -o CMakeFiles/ost_mol.dir/view_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/view_op.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/extent.cc:31: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/extent.cc:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_source.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_source.cc.o -MF CMakeFiles/ost_mol.dir/coord_source.cc.o.d -o CMakeFiles/ost_mol.dir/coord_source.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/coord_source.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/query_view_wrapper.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/query_view_wrapper.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/view_op.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/view_op.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/view_op.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/torsion_handle.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/torsion_handle.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/torsion_handle.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o -MF CMakeFiles/ost_img.dir/image_factory.cc.o.d -o CMakeFiles/ost_img.dir/image_factory.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_factory.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o -MF CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o.d -o CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o -MF CMakeFiles/ost_mol.dir/bounding_box.cc.o.d -o CMakeFiles/ost_mol.dir/bounding_box.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/bounding_box.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o -MF CMakeFiles/ost_mol.dir/xcs_editor.cc.o.d -o CMakeFiles/ost_mol.dir/xcs_editor.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/xcs_editor.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/coord_source.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/coord_source.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.cc:1: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/coord_source.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_factory.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_factory.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_factory.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/xcs_editor.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/xcs_editor.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/xcs_editor.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/bounding_box.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/eigen3/Eigen/src/Core/util/Macros.h:679, from /usr/include/eigen3/Eigen/Core:19, from /usr/include/eigen3/Eigen/Eigenvalues:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/bounding_box.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log_sink.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log_sink.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -MF CMakeFiles/ost_mol.dir/impl/dihedral.cc.o.d -o CMakeFiles/ost_mol.dir/impl/dihedral.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.cc [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_handle.cc.o -MF CMakeFiles/ost_img.dir/image_handle.cc.o.d -o CMakeFiles/ost_img.dir/image_handle.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_handle.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/weak_ptr.hpp:16, from /usr/include/boost/smart_ptr/enable_shared_from_this.hpp:16, from /usr/include/boost/enable_shared_from_this.hpp:16, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_ast.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_ast.cc.o -MF CMakeFiles/ost_mol.dir/impl/query_ast.cc.o.d -o CMakeFiles/ost_mol.dir/impl/query_ast.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/query_ast.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_handle.hh:38, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_handle.cc:31: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_handle.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc:35: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/query_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/query_impl.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.cc In file included from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc:40: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -MF CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o.d -o CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/c++ -DOST_MODULE_OST_MOL -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -MF CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o.d -o CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/atom_prop.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o -MF CMakeFiles/ost_img.dir/image_impl.cc.o.d -o CMakeFiles/ost_img.dir/image_impl.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_impl.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log_sink.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh:36, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod/CMakeFiles/_ost_base.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 11%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o -MF CMakeFiles/_ost_base.dir/wrap_base.cc.o.d -o CMakeFiles/_ost_base.dir/wrap_base.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/pymod/wrap_base.cc [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o -MF CMakeFiles/ost_img.dir/image_list.cc.o.d -o CMakeFiles/ost_img.dir/image_list.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_list.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state_fw.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_impl.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_impl.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_list.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_list.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_list.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/inverted_mask.cc.o -MF CMakeFiles/ost_img.dir/inverted_mask.cc.o.d -o CMakeFiles/ost_img.dir/inverted_mask.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/inverted_mask.cc [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o -MF CMakeFiles/ost_img.dir/map.cc.o.d -o CMakeFiles/ost_img.dir/map.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/map.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/inverted_mask.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/inverted_mask.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o -MF CMakeFiles/ost_img.dir/mask_base.cc.o.d -o CMakeFiles/ost_img.dir/mask_base.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask_base.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/base/pymod/wrap_base.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/map.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/map.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:32: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_op.cc.o -MF CMakeFiles/ost_img.dir/mask_op.cc.o.d -o CMakeFiles/ost_img.dir/mask_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask_op.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask_base.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask.cc.o -MF CMakeFiles/ost_img.dir/mask.cc.o.d -o CMakeFiles/ost_img.dir/mask.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask.cc [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/observable.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/observable.cc.o -MF CMakeFiles/ost_img.dir/observable.cc.o.d -o CMakeFiles/ost_img.dir/observable.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/observable.cc [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o -MF CMakeFiles/ost_img.dir/paste_impl.cc.o.d -o CMakeFiles/ost_img.dir/paste_impl.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/paste_impl.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/composite_mask.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask_op.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/scoped_ptr.hpp:22, from /usr/include/boost/scoped_ptr.hpp:13, from /usr/include/boost/smart_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask_base_fw.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask_op.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask_op.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 12%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_logger.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_logger.cc.o -MF CMakeFiles/_ost_base.dir/export_logger.cc.o.d -o CMakeFiles/_ost_base.dir/export_logger.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/pymod/export_logger.cc [ 12%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o -MF CMakeFiles/ost_img.dir/peak.cc.o.d -o CMakeFiles/ost_img.dir/peak.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/peak.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/observable.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/observable.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/list:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/observable.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/polygon_mask.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask.hh:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 13%] Linking CXX shared library ../../../../stage/lib/libost_mol.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol.so.2.3 -o ../../../../stage/lib/libost_mol.so.2.3.1 CMakeFiles/ost_mol.dir/atom_base.cc.o CMakeFiles/ost_mol.dir/atom_handle.cc.o CMakeFiles/ost_mol.dir/atom_view.cc.o CMakeFiles/ost_mol.dir/bond_handle.cc.o CMakeFiles/ost_mol.dir/chain_base.cc.o CMakeFiles/ost_mol.dir/chain_handle.cc.o CMakeFiles/ost_mol.dir/chain_view.cc.o CMakeFiles/ost_mol.dir/chain_type.cc.o CMakeFiles/ost_mol.dir/coord_frame.cc.o CMakeFiles/ost_mol.dir/coord_group.cc.o CMakeFiles/ost_mol.dir/editor_base.cc.o CMakeFiles/ost_mol.dir/entity_base.cc.o CMakeFiles/ost_mol.dir/entity_handle.cc.o CMakeFiles/ost_mol.dir/entity_observer.cc.o CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o CMakeFiles/ost_mol.dir/entity_view.cc.o CMakeFiles/ost_mol.dir/entity_visitor.cc.o CMakeFiles/ost_mol.dir/ics_editor.cc.o CMakeFiles/ost_mol.dir/not_connected_error.cc.o CMakeFiles/ost_mol.dir/property_id.cc.o CMakeFiles/ost_mol.dir/query.cc.o CMakeFiles/ost_mol.dir/query_error.cc.o CMakeFiles/ost_mol.dir/query_state.cc.o CMakeFiles/ost_mol.dir/residue_base.cc.o CMakeFiles/ost_mol.dir/residue_handle.cc.o CMakeFiles/ost_mol.dir/residue_view.cc.o CMakeFiles/ost_mol.dir/surface_builder.cc.o CMakeFiles/ost_mol.dir/surface_handle.cc.o CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o CMakeFiles/ost_mol.dir/torsion_handle.cc.o CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o CMakeFiles/ost_mol.dir/view_op.cc.o CMakeFiles/ost_mol.dir/coord_source.cc.o CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o CMakeFiles/ost_mol.dir/bounding_box.cc.o CMakeFiles/ost_mol.dir/xcs_editor.cc.o CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o CMakeFiles/ost_mol.dir/impl/dihedral.cc.o CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o CMakeFiles/ost_mol.dir/impl/query_ast.cc.o CMakeFiles/ost_mol.dir/impl/query_impl.cc.o CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 [ 13%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/phase.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/phase.cc.o -MF CMakeFiles/ost_img.dir/phase.cc.o.d -o CMakeFiles/ost_img.dir/phase.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/phase.cc [ 13%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o -MF CMakeFiles/ost_img.dir/physical_units.cc.o.d -o CMakeFiles/ost_img.dir/physical_units.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/physical_units.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3 ../../../../stage/lib/libost_mol.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 13%] Built target ost_mol [ 13%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/pixel_sampling.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/pixel_sampling.cc.o -MF CMakeFiles/ost_img.dir/pixel_sampling.cc.o.d -o CMakeFiles/ost_img.dir/pixel_sampling.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/pixel_sampling.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/peak.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/peak.cc:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/peak.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 13%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o -MF CMakeFiles/ost_img.dir/point_list.cc.o.d -o CMakeFiles/ost_img.dir/point_list.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point_list.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_algorithm.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/paste_impl.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/paste_impl.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:32: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/depend [ 13%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o -MF CMakeFiles/_ost_base.dir/export_range.cc.o.d -o CMakeFiles/_ost_base.dir/export_range.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/pymod/export_range.cc [ 13%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/point.cc.o -MF CMakeFiles/ost_img.dir/point.cc.o.d -o CMakeFiles/ost_img.dir/point.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point.cc make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 13%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -MF CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o.d -o CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point_list.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point_list.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/pixel_sampling.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/pixel_sampling.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 13%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o -MF CMakeFiles/ost_img.dir/polygon_mask.cc.o.d -o CMakeFiles/ost_img.dir/polygon_mask.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/polygon_mask.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point.cc:31: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/base/pymod/export_logger.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 15%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o -MF CMakeFiles/ost_img.dir/progress.cc.o.d -o CMakeFiles/ost_img.dir/progress.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/progress.cc [ 15%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o -MF CMakeFiles/ost_img.dir/size.cc.o.d -o CMakeFiles/ost_img.dir/size.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/size.cc [ 15%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o -MF CMakeFiles/ost_img.dir/spherical_mask.cc.o.d -o CMakeFiles/ost_img.dir/spherical_mask.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/spherical_mask.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/polygon_mask.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/polygon_mask.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/algorithm:60, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/polygon_mask.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /usr/include/boost/format.hpp:17, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 15%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_info_convert.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/mask_info_convert.cc.o -MF CMakeFiles/ost_img.dir/mask_info_convert.cc.o.d -o CMakeFiles/ost_img.dir/mask_info_convert.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask_info_convert.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/spherical_mask.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/spherical_mask.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/size.cc:32: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/size.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 15%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -MF CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o.d -o CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.cc [ 15%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o -MF CMakeFiles/ost_img.dir/image_state/index.cc.o.d -o CMakeFiles/ost_img.dir/image_state/index.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/index.cc [ 15%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -MF CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o.d -o CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/base/pymod/export_range.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 15%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/c++ -DOST_MODULE_OST_IMG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/src/CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -MF CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o.d -o CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask_info_convert.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/deque:60, from /usr/include/c++/12/stack:60, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/mask_info_convert.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data_types.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 15%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o -MF CMakeFiles/_ost_base.dir/export_units.cc.o.d -o CMakeFiles/_ost_base.dir/export_units.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/pymod/export_units.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base_fw.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.cc:38: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.cc:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 15%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -MF CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o.d -o CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.cc [ 16%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_handle.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_handle.cc.o -MF CMakeFiles/ost_seq.dir/sequence_handle.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_handle.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/sequence_handle.cc [ 16%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o -MF CMakeFiles/ost_seq.dir/aligned_region.cc.o.d -o CMakeFiles/ost_seq.dir/aligned_region.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/aligned_region.cc [ 16%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_column.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_column.cc.o -MF CMakeFiles/ost_seq.dir/aligned_column.cc.o.d -o CMakeFiles/ost_seq.dir/aligned_column.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/aligned_column.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info_handle.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_region.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/aligned_region.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/integrity_error.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/aligned_region.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_region.hh:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/sequence_handle.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/aligned_column.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/base/pymod/export_units.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 16%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.cc.o -MF CMakeFiles/ost_seq.dir/sequence_list.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_list.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc [ 16%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/alignment_handle.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/alignment_handle.cc.o -MF CMakeFiles/ost_seq.dir/alignment_handle.cc.o.d -o CMakeFiles/ost_seq.dir/alignment_handle.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/alignment_handle.cc [ 16%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_op.cc.o -MF CMakeFiles/ost_seq.dir/sequence_op.cc.o.d -o CMakeFiles/ost_seq.dir/sequence_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/sequence_op.cc [ 16%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/views_from_sequences.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/views_from_sequences.cc.o -MF CMakeFiles/ost_seq.dir/views_from_sequences.cc.o.d -o CMakeFiles/ost_seq.dir/views_from_sequences.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/views_from_sequences.cc [ 16%] Linking CXX shared library ../../../../stage/lib/libost_img.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_img.so.2.3 -o ../../../../stage/lib/libost_img.so.2.3.1 CMakeFiles/ost_img.dir/circle_mask.cc.o CMakeFiles/ost_img.dir/composite_mask.cc.o CMakeFiles/ost_img.dir/data_algorithm.cc.o CMakeFiles/ost_img.dir/data_observer.cc.o CMakeFiles/ost_img.dir/data.cc.o CMakeFiles/ost_img.dir/extent_iterator.cc.o CMakeFiles/ost_img.dir/extent_mask.cc.o CMakeFiles/ost_img.dir/extent.cc.o CMakeFiles/ost_img.dir/image_factory.cc.o CMakeFiles/ost_img.dir/image_handle.cc.o CMakeFiles/ost_img.dir/image_impl.cc.o CMakeFiles/ost_img.dir/image_list.cc.o CMakeFiles/ost_img.dir/inverted_mask.cc.o CMakeFiles/ost_img.dir/map.cc.o CMakeFiles/ost_img.dir/mask_base.cc.o CMakeFiles/ost_img.dir/mask_op.cc.o CMakeFiles/ost_img.dir/mask.cc.o CMakeFiles/ost_img.dir/observable.cc.o CMakeFiles/ost_img.dir/paste_impl.cc.o CMakeFiles/ost_img.dir/peak.cc.o CMakeFiles/ost_img.dir/phase.cc.o CMakeFiles/ost_img.dir/physical_units.cc.o CMakeFiles/ost_img.dir/pixel_sampling.cc.o CMakeFiles/ost_img.dir/point_list.cc.o CMakeFiles/ost_img.dir/point.cc.o CMakeFiles/ost_img.dir/polygon_mask.cc.o CMakeFiles/ost_img.dir/progress.cc.o CMakeFiles/ost_img.dir/size.cc.o CMakeFiles/ost_img.dir/spherical_mask.cc.o CMakeFiles/ost_img.dir/mask_info_convert.cc.o CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o CMakeFiles/ost_img.dir/image_state/index.cc.o CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 [ 16%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/profile_handle.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/src/CMakeFiles/ost_seq.dir/profile_handle.cc.o -MF CMakeFiles/ost_seq.dir/profile_handle.cc.o.d -o CMakeFiles/ost_seq.dir/profile_handle.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/profile_handle.cc In file included from /usr/include/boost/bind.hpp:30, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/sequence_op.cc:22: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3 ../../../../stage/lib/libost_img.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 16%] Built target ost_img make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -MF CMakeFiles/ost_img_alg.dir/anisotropic.cc.o.d -o CMakeFiles/ost_img_alg.dir/anisotropic.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/anisotropic.cc [ 16%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/auto_correlate.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/alignment_handle.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/alignment_handle.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/alignment_handle.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/sequence_op.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/sequence_op.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/alignment_handle.cc:32: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/views_from_sequences.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/views_from_sequences.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/integrity_error.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/views_from_sequences.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc:31: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/convolute.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/convolute.cc.o -MF CMakeFiles/ost_img_alg.dir/convolute.cc.o.d -o CMakeFiles/ost_img_alg.dir/convolute.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/convolute.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/gaussian.hh:36, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/anisotropic.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/anisotropic.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/anisotropic.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/correlate.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/correlate.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/correlate.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/fft.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/auto_correlate.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/auto_correlate.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o -MF CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o.d -o CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/cross_correlate.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/density_slice.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/density_slice.cc.o -MF CMakeFiles/ost_img_alg.dir/density_slice.cc.o.d -o CMakeFiles/ost_img_alg.dir/density_slice.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/density_slice.cc [ 17%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/_ost_base.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_base.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/_ost_base.so CMakeFiles/_ost_base.dir/wrap_base.cc.o CMakeFiles/_ost_base.dir/export_logger.cc.o CMakeFiles/_ost_base.dir/export_range.cc.o CMakeFiles/_ost_base.dir/export_units.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../stage/lib/libost_base.so.2.3.1 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o -MF CMakeFiles/ost_img_alg.dir/dft.cc.o.d -o CMakeFiles/ost_img_alg.dir/dft.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/dft.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/convolute.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/convolute.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/base/pymod/settings.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/./settings.pyc\",\"settings.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/base/pymod/stutil.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.pyc\",\"stutil.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/base/pymod/table.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table.pyc\",\"table.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/base/pymod/table_selector.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table_selector.pyc\",\"table_selector.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/base/pymod/xmlrunner.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.pyc\",\"xmlrunner.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/base/pymod/testutils.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/./testutils.pyc\",\"testutils.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 17%] Built target _ost_base make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/info/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/pymod/CMakeFiles/_ost_info.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o -MF CMakeFiles/ost_img_alg.dir/fft.cc.o.d -o CMakeFiles/ost_img_alg.dir/fft.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/fft.cc [ 17%] Building CXX object modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_info_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o -MF CMakeFiles/_ost_info.dir/wrap_info.cc.o.d -o CMakeFiles/_ost_info.dir/wrap_info.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/info/pymod/wrap_info.cc [ 17%] Linking CXX shared library ../../../../stage/lib/libost_seq.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_seq.so.2.3 -o ../../../../stage/lib/libost_seq.so.2.3.1 CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o CMakeFiles/ost_seq.dir/sequence_handle.cc.o CMakeFiles/ost_seq.dir/aligned_region.cc.o CMakeFiles/ost_seq.dir/aligned_column.cc.o CMakeFiles/ost_seq.dir/sequence_list.cc.o CMakeFiles/ost_seq.dir/alignment_handle.cc.o CMakeFiles/ost_seq.dir/sequence_op.cc.o CMakeFiles/ost_seq.dir/views_from_sequences.cc.o CMakeFiles/ost_seq.dir/profile_handle.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3 ../../../../stage/lib/libost_seq.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 17%] Built target ost_seq make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/bindings/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 17%] Building CXX object modules/bindings/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/src && /usr/bin/c++ -DOST_MODULE_OST_BINDINGS -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_bindings_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -MF CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o.d -o CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/bindings/src/wrap_tmalign.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/correlate.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/correlate.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/cross_correlate.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/cross_correlate.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/dft.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/dft.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/density_slice.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/density_slice.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o -MF CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o.d -o CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/fourier_filters.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/fft.cc:36: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/fft.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/bindings/wrap_tmalign.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/bindings/src/wrap_tmalign.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /build/reproducible-path/openstructure-2.3.1/modules/bindings/src/tmalign/param_set.h:6, from /build/reproducible-path/openstructure-2.3.1/modules/bindings/src/tmalign/TMalign.h:4, from /build/reproducible-path/openstructure-2.3.1/modules/bindings/src/wrap_tmalign.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian.cc.o /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/gaussian.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/gaussian_gradient_magnitude.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o -MF CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o.d -o CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.cc [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o -MF CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o.d -o CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/highest_peak_search_3d.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/fft.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/fourier_filters.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/fourier_filters.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/info/pymod/wrap_info.cc:27: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/histogram.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/histogram.cc.o -MF CMakeFiles/ost_img_alg.dir/histogram.cc.o.d -o CMakeFiles/ost_img_alg.dir/histogram.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/histogram.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/gaussian.hh:36, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/gaussian.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/gaussian.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/gaussian_gradient_magnitude.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/gaussian_gradient_magnitude.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/gaussian_gradient_magnitude.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/info/pymod/wrap_info.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/stat.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/highest_peak_search_3d.cc:4: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/highest_peak_search_3d.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/stat.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/histogram.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/histogram.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_iterator.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_iterator.cc.o -MF CMakeFiles/ost_img_alg.dir/line_iterator.cc.o.d -o CMakeFiles/ost_img_alg.dir/line_iterator.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/line_iterator.cc [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o -MF CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o.d -o CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/local_sigma_threshold.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/line_iterator.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/line_iterator.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/mask_image.cc.o -MF CMakeFiles/ost_img_alg.dir/mask_image.cc.o.d -o CMakeFiles/ost_img_alg.dir/mask_image.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/mask_image.cc [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer.cc.o -MF CMakeFiles/ost_img_alg.dir/normalizer.cc.o.d -o CMakeFiles/ost_img_alg.dir/normalizer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/normalizer.cc [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -MF CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o.d -o CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/normalizer_factory.cc [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_linear.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_linear.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/norm_linear.cc [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_log.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_log.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/norm_log.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/normalizer.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/normalizer.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/mask_image.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/local_sigma_threshold.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/local_sigma_threshold.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/local_sigma_threshold.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/stat_min_max.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/normalizer_factory.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 18%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o -MF CMakeFiles/ost_img_alg.dir/norm_od.cc.o.d -o CMakeFiles/ost_img_alg.dir/norm_od.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/norm_od.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/norm_linear.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/norm_linear.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -MF CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o.d -o CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/power_spectrum.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/norm_log.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/norm_log.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o -MF CMakeFiles/ost_img_alg.dir/randomize.cc.o.d -o CMakeFiles/ost_img_alg.dir/randomize.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/randomize.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o -MF CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o.d -o CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/smooth_mask_image.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat.cc.o -MF CMakeFiles/ost_img_alg.dir/stat.cc.o.d -o CMakeFiles/ost_img_alg.dir/stat.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/stat.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o -MF CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o.d -o CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/stat_min_max.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/fft.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/power_spectrum.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/power_spectrum.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/norm_od.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/norm_od.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/randomize.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/randomize.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/smooth_mask_image.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_transform.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_transform.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/alg_transform.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/alg_mirror.cc [ 20%] Linking CXX shared library ../../../stage/lib/libost_bindings.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_bindings.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_bindings.so.2.3 -o ../../../stage/lib/libost_bindings.so.2.3.1 CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_bindings.so.2.3.1 ../../../stage/lib/libost_bindings.so.2.3 ../../../stage/lib/libost_bindings.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 20%] Built target ost_bindings make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/db/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src/CMakeFiles/ost_db.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 20%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/sqlite_wrap.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/c++ -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -MF CMakeFiles/ost_db.dir/sqlite_wrap.cc.o.d -o CMakeFiles/ost_db.dir/sqlite_wrap.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/db/src/sqlite_wrap.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/stat_min_max.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/stat_min_max.cc:32: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/stat_min_max.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_shift.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_shift.cc.o -MF CMakeFiles/ost_img_alg.dir/alg_shift.cc.o.d -o CMakeFiles/ost_img_alg.dir/alg_shift.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/alg_shift.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/stat.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/stat.cc:32: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/stat.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o [ 20%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/linear_indexer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/c++ -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/linear_indexer.cc.o -MF CMakeFiles/ost_db.dir/linear_indexer.cc.o.d -o CMakeFiles/ost_db.dir/linear_indexer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/db/src/linear_indexer.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o -MF CMakeFiles/ost_img_alg.dir/threshold.cc.o.d -o CMakeFiles/ost_img_alg.dir/threshold.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/threshold.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/alg_transform.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/alg_transform.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -MF CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o.d -o CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/alg_mirror.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/alg_mirror.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -MF CMakeFiles/ost_img_alg.dir/transformation_base.cc.o.d -o CMakeFiles/ost_img_alg.dir/transformation_base.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/transformation_base.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/alg_shift.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/alg_shift.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/threshold.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/threshold.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformations.cc.o [ 22%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/binary_container.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformations.cc.o -MF CMakeFiles/ost_img_alg.dir/transformations.cc.o.d -o CMakeFiles/ost_img_alg.dir/transformations.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/transformations.cc [ 22%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/extract_data_helper.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/c++ -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/binary_container.cc.o -MF CMakeFiles/ost_db.dir/binary_container.cc.o.d -o CMakeFiles/ost_db.dir/binary_container.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/db/src/binary_container.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/c++ -DOST_MODULE_OST_DB -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -DSQLITE_OMIT_LOAD_EXTENSION -Dost_db_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/src/CMakeFiles/ost_db.dir/extract_data_helper.cc.o -MF CMakeFiles/ost_db.dir/extract_data_helper.cc.o.d -o CMakeFiles/ost_db.dir/extract_data_helper.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/db/src/extract_data_helper.cc [ 22%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -MF CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o.d -o CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/fractional_shift.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/transformation_base.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/transformation_base.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/transformation_base.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 22%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o -MF CMakeFiles/ost_img_alg.dir/polar.cc.o.d -o CMakeFiles/ost_img_alg.dir/polar.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/polar.cc [ 22%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -MF CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o.d -o CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/rscrosscorr.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/transformation_base.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/transformations.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/transformations.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/transformations.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/fft.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/fractional_shift.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/fractional_shift.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/extract_data_helper.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/db/src/extract_data_helper.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/extract_data_helper.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/extract_data_helper.hh:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 22%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/c++ -DOST_MODULE_OST_IMG_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o -MF CMakeFiles/ost_img_alg.dir/line_average.cc.o.d -o CMakeFiles/ost_img_alg.dir/line_average.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/line_average.cc make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 22%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o -MF CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o.d -o CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/clip_alignment.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/conservation.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/conservation.cc.o -MF CMakeFiles/ost_seq_alg.dir/conservation.cc.o.d -o CMakeFiles/ost_seq_alg.dir/conservation.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/conservation.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/polar.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/polar.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/polar.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/rscrosscorr.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o -MF CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o.d -o CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/contact_prediction_score.cc [ 24%] Linking CXX shared library ../../../stage/lib/libost_db.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_db.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_db.so.2.3 -o ../../../stage/lib/libost_db.so.2.3.1 CMakeFiles/ost_db.dir/sqlite_wrap.cc.o CMakeFiles/ost_db.dir/linear_indexer.cc.o CMakeFiles/ost_db.dir/binary_container.cc.o CMakeFiles/ost_db.dir/extract_data_helper.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: /usr/lib/i386-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_db.so.2.3.1 ../../../stage/lib/libost_db.so.2.3 ../../../stage/lib/libost_db.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 24%] Built target ost_db make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/conop/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src/CMakeFiles/ost_conop.dir/DependInfo.cmake --color= In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/clip_alignment.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/clip_alignment.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/clip_alignment.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 24%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/processor.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/processor.cc.o -MF CMakeFiles/ost_conop.dir/processor.cc.o.d -o CMakeFiles/ost_conop.dir/processor.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/src/processor.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/contact_weight_matrix.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/line_average.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/line_average.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/distance_map.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/distance_map.cc.o -MF CMakeFiles/ost_seq_alg.dir/distance_map.cc.o.d -o CMakeFiles/ost_seq_alg.dir/distance_map.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/distance_map.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/conservation.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/entropy.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/entropy.cc.o -MF CMakeFiles/ost_seq_alg.dir/entropy.cc.o.d -o CMakeFiles/ost_seq_alg.dir/entropy.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/entropy.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/contact_prediction_score.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/global_align.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/global_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/global_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/global_align.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/global_align.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/processor.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/processor.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/complex:45, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:26: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)' at /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:27: /usr/include/boost/variant/variant.hpp: In function 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/12/ios:40: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)' at /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[8]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)' at /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)' at /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)' at /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)' at /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/conservation.cc:128:27: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::vector ost::seq::alg::Conservation(const ost::seq::AlignmentHandle&, bool, const String&, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/ins_del.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/ins_del.cc.o -MF CMakeFiles/ost_seq_alg.dir/ins_del.cc.o.d -o CMakeFiles/ost_seq_alg.dir/ins_del.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/ins_del.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/distance_map.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/distance_map.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/distance_map.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/entropy.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/entropy.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/entropy.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/entropy.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/global_align.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/local_align.cc.o /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/local_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/local_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/local_align.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/local_align.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o -MF CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o.d -o CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/merge_pairwise_alignments.cc [ 24%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/pair_subst_weight_matrix.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/ins_del.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/local_align.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/merge_pairwise_alignments.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/merge_pairwise_alignments.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/merge_pairwise_alignments.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o -MF CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o.d -o CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/sequence_similarity.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/impl/align_impl.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/semiglobal_align.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/semiglobal_align.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 26%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/info/_ost_info.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_info.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/info/_ost_info.so CMakeFiles/_ost_info.dir/wrap_info.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so [ 26%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/c++ -DOST_MODULE_OST_SEQ_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o -MF CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o.d -o CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/subst_weight_matrix.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/info/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/info/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 26%] Built target _ost_info make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom.cc.o -MF CMakeFiles/_ost_mol.dir/export_atom.cc.o.d -o CMakeFiles/_ost_mol.dir/export_atom.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_atom.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/sequence_identity.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/variance_map.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/distance_map.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/variance_map.cc:31: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/hmm_score.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/hmm_score.cc:1: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/profile_handle.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/hmm_score.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/amino_acids.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/amino_acids.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/set:60, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/amino_acids.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/conop/src/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/conop.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/compound_lib_base.hh:5, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/minimal_compound_lib.hh:5, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/minimal_compound_lib.cc:1: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/compound.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/compound_lib_base.hh:4: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_atom.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/compound_lib_base.hh:5, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/compound_lib_base.cc:1: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/compound.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/compound_lib_base.hh:4: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_atom.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/heuristic.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/heuristic.cc.o -MF CMakeFiles/ost_conop.dir/heuristic.cc.o.d -o CMakeFiles/ost_conop.dir/heuristic.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/src/heuristic.cc [ 27%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/diag.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/diag.cc.o -MF CMakeFiles/ost_conop.dir/diag.cc.o.d -o CMakeFiles/ost_conop.dir/diag.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/src/diag.cc [ 27%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/rule_based.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/rule_based.cc.o -MF CMakeFiles/ost_conop.dir/rule_based.cc.o.d -o CMakeFiles/ost_conop.dir/rule_based.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/src/rule_based.cc [ 27%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/model_check.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/model_check.cc.o -MF CMakeFiles/ost_conop.dir/model_check.cc.o.d -o CMakeFiles/ost_conop.dir/model_check.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/src/model_check.cc [ 27%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o -MF CMakeFiles/ost_conop.dir/compound.cc.o.d -o CMakeFiles/ost_conop.dir/compound.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/src/compound.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/heuristic.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/heuristic.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/c++ -DOST_MODULE_OST_CONOP -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib.cc.o -MF CMakeFiles/ost_conop.dir/compound_lib.cc.o.d -o CMakeFiles/ost_conop.dir/compound_lib.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/src/compound_lib.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/diag.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/diag.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/diag.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/rule_based.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/rule_based.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/model_check.hh:4, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/model_check.cc:1: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/model_check.cc:2: /build/reproducible-path/openstructure-2.3.1/modules/conop/src/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/compound_lib.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Linking CXX shared library ../../../../stage/lib/libost_seq_alg.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_seq_alg.so.2.3 -o ../../../../stage/lib/libost_seq_alg.so.2.3.1 CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o CMakeFiles/ost_seq_alg.dir/conservation.cc.o CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o CMakeFiles/ost_seq_alg.dir/contact_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/distance_map.cc.o CMakeFiles/ost_seq_alg.dir/entropy.cc.o CMakeFiles/ost_seq_alg.dir/global_align.cc.o CMakeFiles/ost_seq_alg.dir/ins_del.cc.o CMakeFiles/ost_seq_alg.dir/local_align.cc.o CMakeFiles/ost_seq_alg.dir/merge_pairwise_alignments.cc.o CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o CMakeFiles/ost_seq_alg.dir/sequence_similarity.cc.o CMakeFiles/ost_seq_alg.dir/subst_weight_matrix.cc.o CMakeFiles/ost_seq_alg.dir/variance_map.cc.o CMakeFiles/ost_seq_alg.dir/hmm_pseudo_counts.cc.o CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_seq_alg.so.2.3 ../../../../stage/lib/libost_seq_alg.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 27%] Built target ost_seq_alg make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod/CMakeFiles/_ost_img.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 27%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o -MF CMakeFiles/_ost_img.dir/export_data.cc.o.d -o CMakeFiles/_ost_img.dir/export_data.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_data.cc [ 27%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o -MF CMakeFiles/_ost_mol.dir/export_bond.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bond.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_bond.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/ring_finder.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_chain.cc [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_chain_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_chain_view.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_chain_view.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_atom_view.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_atom_view.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_data.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_bond.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_data.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_bond.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_group.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_group.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_coord_group.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_chain.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_chain.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -MF CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o.d -o CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_coord_frame.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_chain_view.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_chain_view.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o -MF CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o.d -o CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_data_algorithm.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_coord_group.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/coord_group.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_coord_group.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_coord_frame.cc:24: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_coord_frame.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o -MF CMakeFiles/_ost_mol.dir/export_editors.cc.o.d -o CMakeFiles/_ost_mol.dir/export_editors.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_data_algorithm.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_data_algorithm.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc [ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_view.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity_view.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_entity_view.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_extent.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_extent.cc.o -MF CMakeFiles/_ost_img.dir/export_extent.cc.o.d -o CMakeFiles/_ost_img.dir/export_extent.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_extent.cc [ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.cc.o -MF CMakeFiles/_ost_mol.dir/export_property_id.cc.o.d -o CMakeFiles/_ost_mol.dir/export_property_id.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_property_id.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh:27:33: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 27 | class pointer_it : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.cc.o -MF CMakeFiles/_ost_mol.dir/export_query.cc.o.d -o CMakeFiles/_ost_mol.dir/export_query.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_query.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_entity_view.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_entity_view.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_extent.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/wrap_extent_iterator.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_extent.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_property_id.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_query.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.cc.o -MF CMakeFiles/_ost_mol.dir/export_residue.cc.o.d -o CMakeFiles/_ost_mol.dir/export_residue.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_residue.cc /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_property_id.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_query.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_handle.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_handle.cc.o -MF CMakeFiles/_ost_img.dir/export_image_handle.cc.o.d -o CMakeFiles/_ost_img.dir/export_image_handle.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_image_handle.cc [ 30%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_residue_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_residue_view.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_residue_view.cc [ 31%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.cc.o -MF CMakeFiles/_ost_mol.dir/export_surface.cc.o.d -o CMakeFiles/_ost_mol.dir/export_surface.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_surface.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_residue.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 31%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -MF CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o.d -o CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_bounding_box.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_residue.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 31%] Linking CXX shared library ../../../stage/lib/libost_conop.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_conop.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_conop.so.2.3 -o ../../../stage/lib/libost_conop.so.2.3.1 CMakeFiles/ost_conop.dir/processor.cc.o CMakeFiles/ost_conop.dir/amino_acids.cc.o CMakeFiles/ost_conop.dir/conop.cc.o CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o CMakeFiles/ost_conop.dir/compound_lib_base.cc.o CMakeFiles/ost_conop.dir/heuristic.cc.o CMakeFiles/ost_conop.dir/diag.cc.o CMakeFiles/ost_conop.dir/rule_based.cc.o CMakeFiles/ost_conop.dir/model_check.cc.o CMakeFiles/ost_conop.dir/compound.cc.o CMakeFiles/ost_conop.dir/compound_lib.cc.o CMakeFiles/ost_conop.dir/ring_finder.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/i386-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3 ../../../stage/lib/libost_conop.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 31%] Built target ost_conop [ 31%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_peak.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_peak.cc.o -MF CMakeFiles/_ost_img.dir/export_peak.cc.o.d -o CMakeFiles/_ost_img.dir/export_peak.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_peak.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_image_handle.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_residue_view.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_image_handle.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_residue_view.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_bounding_box.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_surface.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_bounding_box.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_surface.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 31%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -MF CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o.d -o CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_query_view_wrapper.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_peak.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/peak.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_peak.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 31%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.cc.o -MF CMakeFiles/_ost_mol.dir/export_torsion.cc.o.d -o CMakeFiles/_ost_mol.dir/export_torsion.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_torsion.cc [ 31%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_visitor.cc.o -MF CMakeFiles/_ost_mol.dir/export_visitor.cc.o.d -o CMakeFiles/_ost_mol.dir/export_visitor.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_visitor.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_query_view_wrapper.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_query_view_wrapper.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_torsion.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 31%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.cc.o -MF CMakeFiles/_ost_img.dir/export_phase.cc.o.d -o CMakeFiles/_ost_img.dir/export_phase.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_phase.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_visitor.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 31%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -MF CMakeFiles/_ost_mol.dir/wrap_mol.cc.o.d -o CMakeFiles/_ost_mol.dir/wrap_mol.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/wrap_mol.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_visitor.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 31%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -MF CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o.d -o CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_entity_property_mapper.cc [ 31%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o -MF CMakeFiles/_ost_img.dir/export_point.cc.o.d -o CMakeFiles/_ost_img.dir/export_point.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_point.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_phase.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 31%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o -MF CMakeFiles/_ost_img.dir/export_progress.cc.o.d -o CMakeFiles/_ost_img.dir/export_progress.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_progress.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/wrap_mol.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 31%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o -MF CMakeFiles/_ost_img.dir/export_raster_image.cc.o.d -o CMakeFiles/_ost_img.dir/export_raster_image.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_raster_image.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/editor_base.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/wrap_mol.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_entity_property_mapper.cc:1: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 31%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.cc.o -MF CMakeFiles/_ost_img.dir/export_size.cc.o.d -o CMakeFiles/_ost_img.dir/export_size.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_size.cc make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 31%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -MF CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o.d -o CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/export_entity_property_mapper.cc:3: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_point.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point_list.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_point.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc:22: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_progress.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gfx/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -MF CMakeFiles/ost_gfx.dir/bitmap_io.cc.o.d -o CMakeFiles/ost_gfx.dir/bitmap_io.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/bitmap_io.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_raster_image.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 31%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_mask.cc.o -MF CMakeFiles/_ost_img.dir/export_mask.cc.o.d -o CMakeFiles/_ost_img.dir/export_mask.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_mask.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_raster_image.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o -MF CMakeFiles/ost_gfx.dir/exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/exporter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/exporter.cc [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/collada_exporter.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/collada_exporter.cc.o -MF CMakeFiles/ost_gfx.dir/collada_exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/collada_exporter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/collada_exporter.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_size.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_size.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 31%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.cc.o -MF CMakeFiles/_ost_img.dir/export_image_list.cc.o.d -o CMakeFiles/_ost_img.dir/export_image_list.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_image_list.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/scene.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/collada_exporter.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/collada_exporter.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/exporter.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 31%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/mol/_ost_mol.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/mol/_ost_mol.so CMakeFiles/_ost_mol.dir/export_atom.cc.o CMakeFiles/_ost_mol.dir/export_atom_view.cc.o CMakeFiles/_ost_mol.dir/export_bond.cc.o CMakeFiles/_ost_mol.dir/export_chain.cc.o CMakeFiles/_ost_mol.dir/export_chain_view.cc.o CMakeFiles/_ost_mol.dir/export_coord_group.cc.o CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o CMakeFiles/_ost_mol.dir/export_editors.cc.o CMakeFiles/_ost_mol.dir/export_entity.cc.o CMakeFiles/_ost_mol.dir/export_entity_view.cc.o CMakeFiles/_ost_mol.dir/export_property_id.cc.o CMakeFiles/_ost_mol.dir/export_query.cc.o CMakeFiles/_ost_mol.dir/export_residue.cc.o CMakeFiles/_ost_mol.dir/export_residue_view.cc.o CMakeFiles/_ost_mol.dir/export_surface.cc.o CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o CMakeFiles/_ost_mol.dir/export_torsion.cc.o CMakeFiles/_ost_mol.dir/export_visitor.cc.o CMakeFiles/_ost_mol.dir/wrap_mol.cc.o CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_mask.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color.cc.o -MF CMakeFiles/ost_gfx.dir/color.cc.o.d -o CMakeFiles/ost_gfx.dir/color.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/polygon_mask.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/mask.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_mask.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/primitives.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/primitives.cc.o -MF CMakeFiles/ost_gfx.dir/primitives.cc.o.d -o CMakeFiles/ost_gfx.dir/primitives.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/primitives.cc [ 31%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/entity.cc.o -MF CMakeFiles/ost_gfx.dir/entity.cc.o.d -o CMakeFiles/ost_gfx.dir/entity.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/entity.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 31%] Built target _ost_mol make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 31%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_sequence.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_sequence.cc.o -MF CMakeFiles/_ost_seq.dir/export_sequence.cc.o.d -o CMakeFiles/_ost_seq.dir/export_sequence.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc [ 32%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -MF CMakeFiles/ost_gfx.dir/symmetry_node.cc.o.d -o CMakeFiles/ost_gfx.dir/symmetry_node.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/symmetry_node.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/primitives.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/primitives.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gl_helper.hh:36, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/primitives.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_image_list.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 34%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.cc.o -MF CMakeFiles/_ost_img.dir/export_map.cc.o.d -o CMakeFiles/_ost_img.dir/export_map.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_map.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_image_list.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/entity.cc:36: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/entity.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/symmetry_node.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/symmetry_node.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gl_helper.hh:36, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/symmetry_node.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_node.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_node.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_node.cc [ 34%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/base/pymod/CMakeFiles/_ost_img.dir/wrap_img.cc.o -MF CMakeFiles/_ost_img.dir/wrap_img.cc.o.d -o CMakeFiles/_ost_img.dir/wrap_img.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/wrap_img.cc [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_object.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_object.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_object.cc In file included from /usr/include/boost/bind.hpp:30, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_node.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_node.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/config/no_tr1/memory.hpp:21, from /usr/include/boost/get_pointer.hpp:14, from /usr/include/boost/bind/mem_fn.hpp:25, from /usr/include/boost/mem_fn.hpp:22, from /usr/include/boost/bind/bind.hpp:26, from /usr/include/boost/bind.hpp:29: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_object.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_object.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/export_map.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc:34: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc:37: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/wrap_img.cc:27: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/wrap_img.cc:33: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_prim.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_prim.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_prim.cc [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -MF CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o.d -o CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_test_object.cc [ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -MF CMakeFiles/ost_mol_alg.dir/clash_score.cc.o.d -o CMakeFiles/ost_mol_alg.dir/clash_score.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/clash_score.cc [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/input.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/input.cc.o -MF CMakeFiles/ost_gfx.dir/input.cc.o.d -o CMakeFiles/ost_gfx.dir/input.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/input.cc [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.cc.o -MF CMakeFiles/ost_gfx.dir/prim_list.cc.o.d -o CMakeFiles/ost_gfx.dir/prim_list.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/prim_list.cc [ 34%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/img/_ost_img.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/img/_ost_img.so CMakeFiles/_ost_img.dir/export_data.cc.o CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o CMakeFiles/_ost_img.dir/export_extent.cc.o CMakeFiles/_ost_img.dir/export_image_handle.cc.o CMakeFiles/_ost_img.dir/export_peak.cc.o CMakeFiles/_ost_img.dir/export_phase.cc.o CMakeFiles/_ost_img.dir/export_point.cc.o CMakeFiles/_ost_img.dir/export_progress.cc.o CMakeFiles/_ost_img.dir/export_raster_image.cc.o CMakeFiles/_ost_img.dir/export_size.cc.o CMakeFiles/_ost_img.dir/export_mask.cc.o CMakeFiles/_ost_img.dir/export_image_list.cc.o CMakeFiles/_ost_img.dir/export_map.cc.o CMakeFiles/_ost_img.dir/wrap_img.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/scene.cc.o -MF CMakeFiles/ost_gfx.dir/scene.cc.o.d -o CMakeFiles/ost_gfx.dir/scene.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/scene.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 34%] Built target _ost_img make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 34%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -MF CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o.d -o CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/wrap_alg.cc [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/selection.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/selection.cc.o -MF CMakeFiles/ost_gfx.dir/selection.cc.o.d -o CMakeFiles/ost_gfx.dir/selection.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/selection.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_prim.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_prim.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_prim.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/clash_score.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/scene.cc:33: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/surface.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/surface.cc.o -MF CMakeFiles/ost_gfx.dir/surface.cc.o.d -o CMakeFiles/ost_gfx.dir/surface.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/surface.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_test_object.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_test_object.cc:31: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/boost/system/error_code.hpp:17, from /usr/include/boost/filesystem/path_traits.hpp:22, from /usr/include/boost/filesystem/path.hpp:26, from /usr/include/boost/filesystem/operations.hpp:26, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gfx_test_object.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/scene.cc:40: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/scene.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/scene.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/prim_list.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/prim_list.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/selection.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/selection.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 34%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -MF CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o.d -o CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/sec_structure_segments.cc [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient.cc.o -MF CMakeFiles/ost_gfx.dir/gradient.cc.o.d -o CMakeFiles/ost_gfx.dir/gradient.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gradient.cc [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient_manager.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient_manager.cc.o -MF CMakeFiles/ost_gfx.dir/gradient_manager.cc.o.d -o CMakeFiles/ost_gfx.dir/gradient_manager.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gradient_manager.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/surface.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/surface.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/sec_structure_segments.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/wrap_alg.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gradient.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gradient.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gradient.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/vertex_array.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/auto_correlate.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/wrap_alg.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gradient_manager.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/boost/system/error_code.hpp:17, from /usr/include/boost/filesystem/path_traits.hpp:22, from /usr/include/boost/filesystem/path.hpp:26, from /usr/include/boost/filesystem/operations.hpp:26, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gradient_manager.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -MF CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o.d -o CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/vertex_array_helper.cc [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/material.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/material.cc.o -MF CMakeFiles/ost_gfx.dir/material.cc.o.d -o CMakeFiles/ost_gfx.dir/material.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/material.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/vertex_array.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /usr/include/boost/format.hpp:17, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/povray.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/povray.cc.o -MF CMakeFiles/ost_gfx.dir/povray.cc.o.d -o CMakeFiles/ost_gfx.dir/povray.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/povray.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc:4: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/iomanip:40, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/vertex_array_helper.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/vertex_array_helper.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/vertex_array_helper.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc:6: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gost_exporter.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -MF CMakeFiles/ost_gfx.dir/gost_exporter.cc.o.d -o CMakeFiles/ost_gfx.dir/gost_exporter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gost_exporter.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/material.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/material.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/iterator:61, from /usr/include/boost/operators.hpp:98, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color.hh:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:1311:8: warning: 'geom::Vec3 ost::gfx::{anonymous}::make_aaline_edge(const geom::Vec2&, const geom::Vec2&, float)' defined but not used [-Wunused-function] 1311 | Vec3 make_aaline_edge(const Vec2& c1, const Vec2& c0, float s) | ^~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:1239:8: warning: 'void ost::gfx::{anonymous}::render_aalines(AALineList&, float, float)' defined but not used [-Wunused-function] 1239 | void render_aalines(AALineList& line_list, float w, float r) | ^~~~~~~~~~~~~~ [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/texture.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/texture.cc.o -MF CMakeFiles/ost_gfx.dir/texture.cc.o.d -o CMakeFiles/ost_gfx.dir/texture.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/texture.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/povray.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/povray.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/povray.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.cc [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/scene.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gost_exporter.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/gost_exporter.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.cc [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.cc [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.cc [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/dyn_cast.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info_handle.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 36%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/distance_test_common.cc [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.cc [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -MF CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.cc [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/dyn_cast.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/distance_test_common.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/distance_test_common.cc:1: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.cc [ 36%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -MF CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o.d -o CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/view_op.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/atom_view.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 36%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:2: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/distance_rmsd_test.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:3: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:53: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.cc [ 37%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o -MF CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o.d -o CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/pymod/export_profile_handle.cc [ 37%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_filter.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_filter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/export_filter.cc [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.cc [ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o -MF CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o.d -o CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/superpose_frames.cc [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -MF CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/entity_fw.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/object/class.hpp:9, from /usr/include/boost/python/class.hpp:13, from /usr/include/boost/python/suite/indexing/indexing_suite.hpp:9, from /usr/include/boost/python/suite/indexing/vector_indexing_suite.hpp:9, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/pymod/export_profile_handle.cc:24: /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/superpose_frames.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/eigen3/Eigen/src/Core/util/Macros.h:679, from /usr/include/eigen3/Eigen/Core:19, from /usr/include/eigen3/Eigen/Eigenvalues:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/superpose_frames.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o -MF CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.cc [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o -MF CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/export_filter.cc:27: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/gaussian.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/filter.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/export_filter.cc:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o -MF CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.cc [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o -MF CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/tabulated_trig.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o -MF CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o -MF CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/render_options.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/line_render_options.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/custom_render_options.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/cpk_render_options.cc [ 39%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o -MF CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o.d -o CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/filter_clashes.cc [ 39%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/wrap_seq.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -MF CMakeFiles/_ost_seq.dir/wrap_seq.cc.o.d -o CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/pymod/wrap_seq.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/render_options.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/input.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/render_options.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/sline_render_options.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/line_trace_render_options.cc [ 39%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/export_normalizer.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/cartoon_render_options.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/filter_clashes.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/filter_clashes.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_iso.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o -MF CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o.d -o CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/trace_render_options.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o -MF CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o.d -o CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/map_iso.cc.o -MF CMakeFiles/ost_gfx.dir/map_iso.cc.o.d -o CMakeFiles/ost_gfx.dir/map_iso.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/map_iso.cc [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_slab.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/map_slab.cc.o -MF CMakeFiles/ost_gfx.dir/map_slab.cc.o.d -o CMakeFiles/ost_gfx.dir/map_slab.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/map_slab.cc [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.cc [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/pymod/wrap_seq.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 40%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/seq/_ost_seq.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_seq.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/seq/_ost_seq.so CMakeFiles/_ost_seq.dir/export_sequence.cc.o CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o CMakeFiles/_ost_seq.dir/wrap_seq.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so /usr/lib/i386-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/seq/base/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 40%] Built target _ost_seq make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 40%] Building CXX object modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_bindings_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o -MF CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o.d -o CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/export_tmalign.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/entity.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/discrete_shrink.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/map_iso.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/map_iso.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/stat.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/map_slab.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/map_slab.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/shared_array.hpp:19, from /usr/include/boost/shared_array.hpp:17, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/export_normalizer.cc:27: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/norm.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/export_normalizer.cc:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_o.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/export_tmalign.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 40%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/export_transcendentals.cc [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o -MF CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_octree.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/bindings/wrap_tmalign.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/export_tmalign.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/vertex_array.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/map_iso_prop.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_o.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/shared_array.hpp:19, from /usr/include/boost/shared_array.hpp:17, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_o.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 40%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/c++ -DOST_MODULE_OST_GFX -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -MF CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o.d -o CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.cc [ 40%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_img_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -MF CMakeFiles/_ost_img_alg.dir/export_polar.cc.o.d -o CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/export_polar.cc [ 40%] Building CXX object modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_bindings_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o -MF CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o.d -o CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/wrap_bindings.cc [ 40%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -MF CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o.d -o CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/construct_cbeta.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_octree.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_octree.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_handle.hh:32: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_construct.h:61, from /usr/include/c++/12/bits/alloc_traits.h:33, from /usr/include/c++/12/ext/alloc_traits.h:34, from /usr/include/c++/12/unordered_map:41, from /usr/include/c++/12/functional:61, from /usr/include/boost/container_hash/hash.hpp:20, from /usr/include/boost/functional/hash.hpp:6, from /usr/include/boost/unordered/unordered_map.hpp:18, from /usr/include/boost/unordered_map.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/trajectory_analysis.cc [ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -MF CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o.d -o CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/structure_analysis.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/construct_cbeta.cc:4: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/construct_cbeta.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -MF CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o.d -o CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/consistency_checks.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/export_transcendentals.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/pdbize.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -MF CMakeFiles/ost_mol_alg.dir/pdbize.cc.o.d -o CMakeFiles/ost_mol_alg.dir/pdbize.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/pdbize.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/structure_analysis.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/structure_analysis.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/trajectory_analysis.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/trajectory_analysis.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 41%] Linking CXX shared library ../../../stage/lib/libost_gfx.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/test_texture.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/textures/test_texture.png cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/glyph_texture.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/textures/glyph_texture.png cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gfx.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_gfx.so.2.3 -o ../../../stage/lib/libost_gfx.so.2.3.1 CMakeFiles/ost_gfx.dir/bitmap_io.cc.o CMakeFiles/ost_gfx.dir/exporter.cc.o CMakeFiles/ost_gfx.dir/collada_exporter.cc.o CMakeFiles/ost_gfx.dir/color.cc.o CMakeFiles/ost_gfx.dir/primitives.cc.o CMakeFiles/ost_gfx.dir/entity.cc.o CMakeFiles/ost_gfx.dir/symmetry_node.cc.o CMakeFiles/ost_gfx.dir/gfx_node.cc.o CMakeFiles/ost_gfx.dir/gfx_object.cc.o CMakeFiles/ost_gfx.dir/gfx_prim.cc.o CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o CMakeFiles/ost_gfx.dir/input.cc.o CMakeFiles/ost_gfx.dir/prim_list.cc.o CMakeFiles/ost_gfx.dir/scene.cc.o CMakeFiles/ost_gfx.dir/selection.cc.o CMakeFiles/ost_gfx.dir/surface.cc.o CMakeFiles/ost_gfx.dir/gradient.cc.o CMakeFiles/ost_gfx.dir/gradient_manager.cc.o CMakeFiles/ost_gfx.dir/vertex_array.cc.o CMakeFiles/ost_gfx.dir/vertex_array_helper.cc.o CMakeFiles/ost_gfx.dir/material.cc.o CMakeFiles/ost_gfx.dir/povray.cc.o CMakeFiles/ost_gfx.dir/gost_exporter.cc.o CMakeFiles/ost_gfx.dir/texture.cc.o CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/custom_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/cpk_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/backbone_trace.cc.o CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o CMakeFiles/ost_gfx.dir/impl/mapped_property.cc.o CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o CMakeFiles/ost_gfx.dir/map_iso.cc.o CMakeFiles/ost_gfx.dir/map_slab.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/i386-linux-gnu/libOpenGL.so /usr/lib/i386-linux-gnu/libGLX.so /usr/lib/i386-linux-gnu/libGLU.so /usr/lib/i386-linux-gnu/libpng.so /usr/lib/i386-linux-gnu/libz.so ../../../stage/lib/libost_db.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/transcendentals.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/export_transcendentals.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/export_polar.cc:24: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/consistency_checks.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/consistency_checks.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/wrap_bindings.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_gfx.so.2.3.1 ../../../stage/lib/libost_gfx.so.2.3 ../../../stage/lib/libost_gfx.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 41%] Built target ost_gfx make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/db/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/pymod/CMakeFiles/_ost_db.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 41%] Building CXX object modules/db/pymod/CMakeFiles/_ost_db.dir/export_linear_db.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_db_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/pymod/CMakeFiles/_ost_db.dir/export_linear_db.cc.o -MF CMakeFiles/_ost_db.dir/export_linear_db.cc.o.d -o CMakeFiles/_ost_db.dir/export_linear_db.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/db/pymod/export_linear_db.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/polar.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/export_polar.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 41%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/bindings/_ost_bindings.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_bindings.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/bindings/_ost_bindings.so CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../stage/lib/libost_bindings.so.2.3.1 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/pdbize.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/pdbize.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./__init__.pyc\",\"__init__.py\",doraise=True)" In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/pdbize.hh:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/lga.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./lga.pyc\",\"lga.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/hbplus.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hbplus.pyc\",\"hbplus.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/msms.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./msms.pyc\",\"msms.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/tmtools.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./tmtools.pyc\",\"tmtools.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/dssp.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dssp.pyc\",\"dssp.py\",doraise=True)" [ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -MF CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o.d -o CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/clustalw.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./clustalw.pyc\",\"clustalw.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/utils.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./utils.pyc\",\"utils.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/naccess.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./naccess.pyc\",\"naccess.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/hhblits.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits.pyc\",\"hhblits.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/hhblits2.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits2.pyc\",\"hhblits2.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/hhblits3.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits3.pyc\",\"hhblits3.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/blast.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./blast.pyc\",\"blast.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/cadscore.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./cadscore.pyc\",\"cadscore.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/kclust.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./kclust.pyc\",\"kclust.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/ialign.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./ialign.pyc\",\"ialign.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod/mmseqs2.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./mmseqs2.pyc\",\"mmseqs2.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 41%] Built target _ost_bindings [ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -MF CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o.d -o CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc [ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/domain_find.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -MF CMakeFiles/ost_mol_alg.dir/domain_find.cc.o.d -o CMakeFiles/ost_mol_alg.dir/domain_find.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc [ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -MF CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o.d -o CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.cc [ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/accessibility.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -MF CMakeFiles/ost_mol_alg.dir/accessibility.cc.o.d -o CMakeFiles/ost_mol_alg.dir/accessibility.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_factory.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_factory.hh:31: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:2: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:3: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.hh:9, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.hh:7, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.cc:1: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.hh:5: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -MF CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o.d -o CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/sec_struct.cc [ 41%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -MF CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o.d -o CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/nonstandard.cc [ 41%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/img/alg/_ost_img_alg.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img_alg.dir/link.txt --verbose=1 make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/depend /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/img/alg/_ost_img_alg.so CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o CMakeFiles/_ost_img_alg.dir/export_filter.cc.o CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o CMakeFiles/_ost_img_alg.dir/export_polar.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 41%] Building CXX object modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_seq_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -MF CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o.d -o CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod/wrap_seq_alg.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/accessibility.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:1: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/db/pymod/export_linear_db.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 41%] Built target _ost_img_alg [ 41%] Building CXX object modules/db/pymod/CMakeFiles/_ost_db.dir/wrap_db.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_db_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/db/pymod/CMakeFiles/_ost_db.dir/wrap_db.cc.o -MF CMakeFiles/_ost_db.dir/wrap_db.cc.o.d -o CMakeFiles/_ost_db.dir/wrap_db.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/db/pymod/wrap_db.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_factory.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:3: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/thread/exceptions.hpp:20, from /usr/include/boost/thread/pthread/thread_data.hpp:10, from /usr/include/boost/thread/thread_only.hpp:17, from /usr/include/boost/thread/thread.hpp:12, from /usr/include/boost/thread.hpp:13, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/extract_data_helper.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/db/pymod/export_linear_db.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/extract_data_helper.hh:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:9: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/sec_struct.cc:1: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:53: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/12/ios:40: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[8]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:66:20: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[8]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:445:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[8]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:448:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[8]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:453:23: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'void ost::mol::alg::DomainsFromCOM(const SimilarityMatrix&, ost::seq::AlignmentHandle, Real, int, int)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/nonstandard.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/nonstandard.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 43%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o -MF CMakeFiles/ost_mol_alg.dir/molck.cc.o.d -o CMakeFiles/ost_mol_alg.dir/molck.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/molck.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/molck.cc:1: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/xcs_editor.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/complex:45, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:24: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_base.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:27: /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 43%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -MF CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o.d -o CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc In file included from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/molck.cc:4: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 43%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_ALG -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -MF CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o.d -o CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/entity_to_density.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/db/pymod/wrap_db.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/merge_pairwise_alignments.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod/wrap_seq_alg.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/ins_del.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod/wrap_seq_alg.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/dft.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/entity_to_density.cc:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/entity_to_density.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 44%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/db/_ost_db.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_db.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/db/_ost_db.so CMakeFiles/_ost_db.dir/export_linear_db.cc.o CMakeFiles/_ost_db.dir/wrap_db.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so /usr/lib/i386-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/db/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/db/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 44%] Built target _ost_db make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod/CMakeFiles/_ost_conop.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 45%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/wrap_conop.cc.o [ 45%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_processor.cc.o [ 45%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_compound.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_compound.cc.o -MF CMakeFiles/_ost_conop.dir/export_compound.cc.o.d -o CMakeFiles/_ost_conop.dir/export_compound.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_compound.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/wrap_conop.cc.o -MF CMakeFiles/_ost_conop.dir/wrap_conop.cc.o.d -o CMakeFiles/_ost_conop.dir/wrap_conop.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/wrap_conop.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_processor.cc.o -MF CMakeFiles/_ost_conop.dir/export_processor.cc.o.d -o CMakeFiles/_ost_conop.dir/export_processor.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_processor.cc [ 45%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_heuristic.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_heuristic.cc.o -MF CMakeFiles/_ost_conop.dir/export_heuristic.cc.o.d -o CMakeFiles/_ost_conop.dir/export_heuristic.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_heuristic.cc [ 45%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o -MF CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o.d -o CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_amino_acids.cc In file included from /usr/include/c++/12/string:53, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /usr/include/c++/12/complex:45, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:24: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:1038:20: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In function 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/12/ios:40: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:1038:20: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[8]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:1038:20: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:1038:20: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:1038:20: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:1038:20: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'Eigen::Matrix {anonymous}::EnergyF::operator()(const Eigen::Matrix&) const', inlined from '{anonymous}::LMInput {anonymous}::GetFinalSolution(const std::__cxx11::list&, Real)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:742:36, inlined from 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:1027:58: /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:243:36: warning: 'best_lm_parameters.Eigen::Matrix::.Eigen::PlainObjectBase >::m_storage.Eigen::DenseStorage::m_data.Eigen::internal::plain_array::array[3]' may be used uninitialized [-Wmaybe-uninitialized] 243 | distance_to_center = std::abs(x(3, 0) - pos_on_axis); | ~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc: In function 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)': /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:697:29: note: 'best_lm_parameters.Eigen::Matrix::.Eigen::PlainObjectBase >::m_storage.Eigen::DenseStorage::m_data.Eigen::internal::plain_array::array[3]' was declared here 697 | Eigen::Matrix best_lm_parameters; | ^~~~~~~~~~~~~~~~~~ In function '{anonymous}::LMInput {anonymous}::GetFinalSolution(const std::__cxx11::list&, Real)', inlined from 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:1027:58: /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:734:23: warning: 'best_lm_parameters.Eigen::Matrix::.Eigen::PlainObjectBase >::m_storage.Eigen::DenseStorage::m_data.Eigen::internal::plain_array::array[2]' may be used uninitialized [-Wmaybe-uninitialized] 734 | sol.mem_param.width = best_lm_parameters(2,0); | ~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc: In function 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)': /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:697:29: note: 'best_lm_parameters.Eigen::Matrix::.Eigen::PlainObjectBase >::m_storage.Eigen::DenseStorage::m_data.Eigen::internal::plain_array::array[2]' was declared here 697 | Eigen::Matrix best_lm_parameters; | ^~~~~~~~~~~~~~~~~~ In member function 'Eigen::Matrix {anonymous}::EnergyF::operator()(const Eigen::Matrix&) const', inlined from '{anonymous}::LMInput {anonymous}::GetFinalSolution(const std::__cxx11::list&, Real)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:742:36, inlined from 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:1027:58: /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:231:35: warning: 'best_lm_parameters.Eigen::Matrix::.Eigen::PlainObjectBase >::m_storage.Eigen::DenseStorage::m_data.Eigen::internal::plain_array::array[1]' may be used uninitialized [-Wmaybe-uninitialized] 231 | tilted_axis = RotateAroundAxis(tilted_axis, axis, x(1, 0)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc: In function 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)': /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:697:29: note: 'best_lm_parameters.Eigen::Matrix::.Eigen::PlainObjectBase >::m_storage.Eigen::DenseStorage::m_data.Eigen::internal::plain_array::array[1]' was declared here 697 | Eigen::Matrix best_lm_parameters; | ^~~~~~~~~~~~~~~~~~ In member function 'Eigen::Matrix {anonymous}::EnergyF::operator()(const Eigen::Matrix&) const', inlined from '{anonymous}::LMInput {anonymous}::GetFinalSolution(const std::__cxx11::list&, Real)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:742:36, inlined from 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:1027:58: /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:230:35: warning: '*(float*)((char*)&best_lm_parameters + offsetof(Eigen::Matrix,Eigen::Matrix::.Eigen::PlainObjectBase >::.Eigen::MatrixBase >::.Eigen::DenseBase >::.Eigen::DenseCoeffsBase, 3>::.Eigen::DenseCoeffsBase, 1>::.Eigen::DenseCoeffsBase, 0>::))' may be used uninitialized [-Wmaybe-uninitialized] 230 | tilted_axis = RotateAroundAxis(tilted_axis, tilt_axis, x(0, 0)); | ~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc: In function 'ost::mol::alg::FindMemParam ost::mol::alg::FindMembrane(ost::mol::EntityView&, bool, bool)': /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:697:29: note: '*(float*)((char*)&best_lm_parameters + offsetof(Eigen::Matrix,Eigen::Matrix::.Eigen::PlainObjectBase >::.Eigen::MatrixBase >::.Eigen::DenseBase >::.Eigen::DenseCoeffsBase, 3>::.Eigen::DenseCoeffsBase, 1>::.Eigen::DenseCoeffsBase, 0>::))' was declared here 697 | Eigen::Matrix best_lm_parameters; | ^~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/wrap_conop.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_heuristic.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_compound.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_processor.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 45%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_conop.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_conop.cc.o -MF CMakeFiles/_ost_conop.dir/export_conop.cc.o.d -o CMakeFiles/_ost_conop.dir/export_conop.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_conop.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/heuristic.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_heuristic.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/processor.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_processor.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_compound.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_amino_acids.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 45%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_diag.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_diag.cc.o -MF CMakeFiles/_ost_conop.dir/export_diag.cc.o.d -o CMakeFiles/_ost_conop.dir/export_diag.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_diag.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/amino_acids.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_amino_acids.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:778:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/12/ios:40: In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[8]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::AtomBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:785:32: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[8]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:788:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:803:35: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:866:17, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/12/bits/basic_string.h:1064:16: warning: '*(const std::__cxx11::basic_string, std::allocator >*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)).std::__cxx11::basic_string::_M_string_length' may be used uninitialized [-Wmaybe-uninitialized] 1064 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In static member function 'static constexpr void std::char_traits::assign(char_type&, const char_type&)', inlined from 'static void std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::_S_copy(_CharT*, const _CharT*, size_type) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:421:23, inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:867:18, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/12/bits/char_traits.h:354:16: warning: '((const std::char_traits::char_type*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[8]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = float; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetFloatProp(const String&, Real) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)' at /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:808:35: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'Real {anonymous}::SetAccessibilityProps(ost::mol::EntityView&, ost::mol::AtomViewList&, const std::vector&, const String&, const String&, const String&, ost::mol::alg::AccessibilityAlgorithm)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_diag.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_conop.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/diag.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_diag.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 45%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_conop_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -MF CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o.d -o CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_ring_finder.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_conop.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 45%] Linking CXX shared library ../../../../stage/lib/libost_mol_alg.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/atom_scattering_properties.txt /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/atom_scattering_properties.txt cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/stereo_chemical_props.txt /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/stereo_chemical_props.txt cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_mol_alg.so.2.3 -o ../../../../stage/lib/libost_mol_alg.so.2.3.1 CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o CMakeFiles/ost_mol_alg.dir/clash_score.cc.o CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o CMakeFiles/ost_mol_alg.dir/structure_analysis.cc.o CMakeFiles/ost_mol_alg.dir/consistency_checks.cc.o CMakeFiles/ost_mol_alg.dir/pdbize.cc.o CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o CMakeFiles/ost_mol_alg.dir/domain_find.cc.o CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o CMakeFiles/ost_mol_alg.dir/accessibility.cc.o CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o CMakeFiles/ost_mol_alg.dir/nonstandard.cc.o CMakeFiles/ost_mol_alg.dir/molck.cc.o CMakeFiles/ost_mol_alg.dir/find_membrane.cc.o CMakeFiles/ost_mol_alg.dir/entity_to_density.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: /usr/lib/i386-linux-gnu/libboost_program_options.so /usr/lib/i386-linux-gnu/libboost_thread.so /usr/lib/i386-linux-gnu/libboost_chrono.so /usr/lib/i386-linux-gnu/libboost_date_time.so /usr/lib/i386-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libsqlite3.so In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_rule_based.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/rule_based.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_rule_based.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3 ../../../../stage/lib/libost_mol_alg.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 45%] Built target ost_mol_alg make -f modules/io/src/CMakeFiles/ost_io.dir/build.make modules/io/src/CMakeFiles/ost_io.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/io/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src/CMakeFiles/ost_io.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/io/src/CMakeFiles/ost_io.dir/build.make modules/io/src/CMakeFiles/ost_io.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 45%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/io_utils.cc.o [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/convert.cc.o [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/io_manager.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/io_utils.cc.o -MF CMakeFiles/ost_io.dir/io_utils.cc.o.d -o CMakeFiles/ost_io.dir/io_utils.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/io_utils.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/io_manager.cc.o -MF CMakeFiles/ost_io.dir/io_manager.cc.o.d -o CMakeFiles/ost_io.dir/io_manager.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/io_manager.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/convert.cc.o -MF CMakeFiles/ost_io.dir/convert.cc.o.d -o CMakeFiles/ost_io.dir/convert.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/convert.cc [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.cc [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_ring_finder.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/ring_finder.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/export_ring_finder.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/io_manager.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/io_manager.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_reader.cc [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.cc:33: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.cc:35: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/conop/_ost_conop.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_conop.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/conop/_ost_conop.so CMakeFiles/_ost_conop.dir/wrap_conop.cc.o CMakeFiles/_ost_conop.dir/export_compound.cc.o CMakeFiles/_ost_conop.dir/export_processor.cc.o CMakeFiles/_ost_conop.dir/export_heuristic.cc.o CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o CMakeFiles/_ost_conop.dir/export_conop.cc.o CMakeFiles/_ost_conop.dir/export_diag.cc.o CMakeFiles/_ost_conop.dir/export_rule_based.cc.o CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../stage/lib/libost_conop.so.2.3.1 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/i386-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.cc:38: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.cc:35: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/conop/pymod/cleanup.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./cleanup.pyc\",\"cleanup.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Built target _ost_conop make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 46%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o -MF CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o.d -o CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/wrap_gfx.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_reader.cc:31: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/algorithm:60, from /usr/include/boost/iostreams/filter/gzip.hpp:21, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_reader.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_reader.cc:34: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_writer.cc [ 46%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/seq/alg/_ost_seq_alg.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_seq_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/seq/alg/_ost_seq_alg.so CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq_alg.so.2.3.1 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod/mat.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./mat.pyc\",\"mat.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod/renumber.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./renumber.pyc\",\"renumber.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod/aaindex.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./aaindex.pyc\",\"aaindex.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 46%] Built target _ost_seq_alg make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 46%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o -MF CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/wrap_mol_alg.cc [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_writer.cc:35: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/locale:39, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_writer.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/wrap_gfx.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/info.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/wrap_gfx.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh:35, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.cc:35: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/sdf_reader.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/wrap_mol_alg.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/wrap_mol_alg.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o -MF CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o.d -o CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/sdf_writer.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/save_entity.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/save_entity.cc.o -MF CMakeFiles/ost_io.dir/mol/save_entity.cc.o.d -o CMakeFiles/ost_io.dir/mol/save_entity.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/save_entity.cc [ 48%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene.cc.o -MF CMakeFiles/_ost_gfx.dir/export_scene.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_scene.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_scene.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/sdf_reader.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/algorithm/string/std/string_traits.hpp:15, from /usr/include/boost/algorithm/string/std_containers_traits.hpp:19, from /usr/include/boost/algorithm/string.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/sdf_reader.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/save_entity.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/save_entity.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh:35, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/sdf_writer.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/format/alt_sstream.hpp:22, from /usr/include/boost/format/internals.hpp:24, from /usr/include/boost/format.hpp:38, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh:33: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/load_entity.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/load_entity.cc.o -MF CMakeFiles/ost_io.dir/mol/load_entity.cc.o.d -o CMakeFiles/ost_io.dir/mol/load_entity.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/load_entity.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o -MF CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o.d -o CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/load_surface.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/load_surface.cc.o -MF CMakeFiles/ost_io.dir/mol/load_surface.cc.o.d -o CMakeFiles/ost_io.dir/mol/load_surface.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/load_surface.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_scene.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o -MF CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o.d -o CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_scene.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/surface.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/surface_io_handler.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/load_surface.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/load_surface.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/load_entity.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/load_entity.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/load_surface.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/load_entity.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.cc:1: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/chem_class.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/io_profile.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/io_profile.cc.o -MF CMakeFiles/ost_io.dir/mol/io_profile.cc.o.d -o CMakeFiles/ost_io.dir/mol/io_profile.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/io_profile.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/dcd_io.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/dcd_io.cc.o -MF CMakeFiles/ost_io.dir/mol/dcd_io.cc.o.d -o CMakeFiles/ost_io.dir/mol/dcd_io.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/dcd_io.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/star_parser.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/star_parser.cc.o -MF CMakeFiles/ost_io.dir/mol/star_parser.cc.o.d -o CMakeFiles/ost_io.dir/mol/star_parser.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/star_parser.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/io_profile.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/io_profile.cc:1: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/io_profile.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 49%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o -MF CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o.d -o CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/mmcif_info.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/dcd_io.cc:33: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/dcd_io.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/profile.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 49%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_str.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_str.cc.o -MF CMakeFiles/ost_io.dir/mol/pdb_str.cc.o.d -o CMakeFiles/ost_io.dir/mol/pdb_str.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_str.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/dcd_io.cc:40: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 49%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o -MF CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o.d -o CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/mmcif_info.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/io_exception.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/mmcif_info.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/stereochemical_params_reader.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/boost/system/error_code.hpp:17, from /usr/include/boost/filesystem/path_traits.hpp:22, from /usr/include/boost/filesystem/path.hpp:26, from /usr/include/boost/filesystem/fstream.hpp:21, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/pdb_str.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_str.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_str.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_str.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 49%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_gfx_node.cc [ 49%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/omf.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/mol/omf.cc.o -MF CMakeFiles/ost_io.dir/mol/omf.cc.o.d -o CMakeFiles/ost_io.dir/mol/omf.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/omf.cc [ 49%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc [ 49%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/load.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/load.cc.o -MF CMakeFiles/ost_io.dir/seq/load.cc.o.d -o CMakeFiles/ost_io.dir/seq/load.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/load.cc [ 49%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/save.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/save.cc.o -MF CMakeFiles/ost_io.dir/seq/save.cc.o.d -o CMakeFiles/ost_io.dir/seq/save.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/save.cc [ 49%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/load.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/load.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/load.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_gfx_node.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/omf.cc:2: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/omf.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mmcif_info.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/omf.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/omf.cc:6: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/save.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/save.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 49%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.cc [ 49%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.cc [ 50%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/hhm_io_handler.cc [ 51%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o -MF CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_symmetry_node.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 51%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o -MF CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o.d -o CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/pssm_io_handler.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_symmetry_node.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/symmetry_node.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_symmetry_node.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 51%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/load_map.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/load_map.cc.o -MF CMakeFiles/ost_io.dir/img/load_map.cc.o.d -o CMakeFiles/ost_io.dir/img/load_map.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/load_map.cc [ 51%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.cc [ 51%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.cc [ 51%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.cc [ 51%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_svd_superpose.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/map.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/load_map.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/load_map.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/load_map.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 51%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.cc:35: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 51%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.cc:37: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.cc:34: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/iomanip:40, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 51%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_gfx_obj.cc [ 51%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_svd_superpose.cc:23: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_svd_superpose.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.cc:76: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.cc:58: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/bind.hpp:30, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:32: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.cc:37: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:34: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:43: /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:51:40: warning: 'int32' is deprecated [-Wdeprecated-declarations] 51 | class complexint32:public std::complex{ | ^~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:24: /usr/include/i386-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:61:40: warning: 'int16' is deprecated [-Wdeprecated-declarations] 61 | class complexint16:public std::complex{ | ^~~~~ /usr/include/i386-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:71:39: warning: 'int8' is deprecated [-Wdeprecated-declarations] 71 | class complexint8:public std::complex{ | ^~~~ /usr/include/i386-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:105:114: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 105 | void do_tiff_read(tdata_t buf,unsigned int rps, unsigned int width, IST* is,unsigned int& current_row, uint16 spp) | ^ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc: In member function 'virtual void ost::io::MapIOTiffHandler::do_export(const ost::img::MapHandle&, TIFF*, ost::io::TIF&) const': /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:310:10: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 310 | uint16 spp=1; | ^~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:311:10: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 311 | uint16 fmt =0; | ^~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:312:10: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 312 | uint16 bpp =0 ; | ^~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:338:40: warning: 'int8' is deprecated [-Wdeprecated-declarations] 338 | fsr=detail::do_tiff_write; | ^~~~ /usr/include/i386-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:343:40: warning: 'int16' is deprecated [-Wdeprecated-declarations] 343 | fsr=detail::do_tiff_write; | ^~~~~ /usr/include/i386-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:348:40: warning: 'int32' is deprecated [-Wdeprecated-declarations] 348 | fsr=detail::do_tiff_write; | ^~~~~ /usr/include/i386-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:363:40: warning: 'int16' is deprecated [-Wdeprecated-declarations] 363 | fsr=detail::do_tiff_write; | ^~~~~ /usr/include/i386-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:371:40: warning: 'uint8' is deprecated [-Wdeprecated-declarations] 371 | fsr=detail::do_tiff_write; | ^~~~~ /usr/include/i386-linux-gnu/tiff.h:80:37: note: declared here 80 | typedef TIFF_MSC_DEPRECATED uint8_t uint8 TIFF_GCC_DEPRECATED; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:376:40: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 376 | fsr=detail::do_tiff_write; | ^~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:381:40: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 381 | fsr=detail::do_tiff_write; | ^~~~~~ /usr/include/i386-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:396:40: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 396 | fsr=detail::do_tiff_write; | ^~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:406:54: warning: 'int8' is deprecated [-Wdeprecated-declarations] 406 | fsc=detail::do_tiff_write,img::image_state::ComplexSpatialImageState>; | ^~~~ /usr/include/i386-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:411:54: warning: 'int16' is deprecated [-Wdeprecated-declarations] 411 | fsc=detail::do_tiff_write,img::image_state::ComplexSpatialImageState>; | ^~~~~ /usr/include/i386-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:416:54: warning: 'int32' is deprecated [-Wdeprecated-declarations] 416 | fsc=detail::do_tiff_write,img::image_state::ComplexSpatialImageState>; | ^~~~~ /usr/include/i386-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc: In member function 'void ost::io::MapIOTiffHandler::load_image_data(TIFF*, ost::img::ImageHandle&, const ost::io::TIF&)': /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:556:10: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 556 | uint16 bpp,spp,plc,ori,reso=RESUNIT_NONE,fmt=SAMPLEFORMAT_UINT; | ^~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:556:14: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 556 | uint16 bpp,spp,plc,ori,reso=RESUNIT_NONE,fmt=SAMPLEFORMAT_UINT; | ^~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:556:18: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 556 | uint16 bpp,spp,plc,ori,reso=RESUNIT_NONE,fmt=SAMPLEFORMAT_UINT; | ^~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:556:22: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 556 | uint16 bpp,spp,plc,ori,reso=RESUNIT_NONE,fmt=SAMPLEFORMAT_UINT; | ^~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:556:26: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 556 | uint16 bpp,spp,plc,ori,reso=RESUNIT_NONE,fmt=SAMPLEFORMAT_UINT; | ^~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:556:44: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 556 | uint16 bpp,spp,plc,ori,reso=RESUNIT_NONE,fmt=SAMPLEFORMAT_UINT; | ^~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:653:30: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 653 | detail::do_tiff_read(buf,rowcount,width,is,current_row,spp); | ^~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:656:30: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 656 | detail::do_tiff_read(buf,rowcount,width,is,current_row,spp); | ^~~~~~ /usr/include/i386-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:662:12: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 662 | uint16 photometric; | ^~~~~~~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:665:17: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 665 | uint16* lookuptable_red; | ^~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:666:17: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 666 | uint16* lookuptable_green; | ^~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:667:17: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 667 | uint16* lookuptable_blue; | ^~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:706:32: warning: 'int8' is deprecated [-Wdeprecated-declarations] 706 | detail::do_tiff_read(buf,rowcount,width,isr,current_row,spp); | ^~~~ /usr/include/i386-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:708:32: warning: 'uint8' is deprecated [-Wdeprecated-declarations] 708 | detail::do_tiff_read(buf,rowcount,width,isr,current_row,spp); | ^~~~~ /usr/include/i386-linux-gnu/tiff.h:80:37: note: declared here 80 | typedef TIFF_MSC_DEPRECATED uint8_t uint8 TIFF_GCC_DEPRECATED; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:717:32: warning: 'int16' is deprecated [-Wdeprecated-declarations] 717 | detail::do_tiff_read(buf,rowcount,width,isr,current_row,spp); | ^~~~~ /usr/include/i386-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:719:32: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 719 | detail::do_tiff_read(buf,rowcount,width,isr,current_row,spp); | ^~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:730:32: warning: 'int32' is deprecated [-Wdeprecated-declarations] 730 | detail::do_tiff_read(buf,rowcount,width,isr,current_row,spp); | ^~~~~ /usr/include/i386-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:732:32: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 732 | detail::do_tiff_read(buf,rowcount,width,isr,current_row,spp); | ^~~~~~ /usr/include/i386-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:771:12: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 771 | uint16 photometric; | ^~~~~~~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:774:17: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 774 | uint16* lookuptable_red; | ^~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:775:17: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 775 | uint16* lookuptable_green; | ^~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:776:17: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 776 | uint16* lookuptable_blue; | ^~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_gfx_obj.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 53%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_clash.cc [ 53%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.cc [ 53%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_gfx_obj.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 54%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/shared_array.hpp:19, from /usr/include/boost/shared_array.hpp:17, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.cc:31: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/iomanip:40, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 54%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/alg_transform.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/transform.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:29: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc:38: /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:51:40: warning: 'int32' is deprecated [-Wdeprecated-declarations] 51 | class complexint32:public std::complex{ | ^~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:24: /usr/include/i386-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:61:40: warning: 'int16' is deprecated [-Wdeprecated-declarations] 61 | class complexint16:public std::complex{ | ^~~~~ /usr/include/i386-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:71:39: warning: 'int8' is deprecated [-Wdeprecated-declarations] 71 | class complexint8:public std::complex{ | ^~~~ /usr/include/i386-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:105:114: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 105 | void do_tiff_read(tdata_t buf,unsigned int rps, unsigned int width, IST* is,unsigned int& current_row, uint16 spp) | ^ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc: In member function 'virtual void ost::io::MapIOJpkHandler::Import(ost::img::ImageHandle&, const boost::filesystem::path&, const ost::io::ImageFormatBase&)': /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc:128:11: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 128 | uint16* reflect; | ^~~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc:129:11: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 129 | uint32* dummy; | ^~~~~ /usr/include/i386-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc: In member function 'virtual void ost::io::MapIOJpkHandler::Import(ost::img::MapHandle&, std::istream&, const ost::io::ImageFormatBase&)': /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc:223:11: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 223 | uint16* reflect; | ^~~~~~~ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc:224:11: warning: 'uint32' is deprecated [-Wdeprecated-declarations] 224 | uint32* dummy; | ^~~~~ /usr/include/i386-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 54%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_clash.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.cc:34: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/fstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 54%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o -MF CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o.d -o CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/clash_score.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_clash.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 54%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/image_format.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/image_format.cc.o -MF CMakeFiles/ost_io.dir/img/image_format.cc.o.d -o CMakeFiles/ost_io.dir/img/image_format.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/image_format.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.cc:34: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.cc:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 54%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_trajectory_analysis.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.cc:34: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/iomanip:40, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 54%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/tiff_util.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/c++ -DOST_MODULE_OST_IO -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/src/CMakeFiles/ost_io.dir/img/tiff_util.cc.o -MF CMakeFiles/ost_io.dir/img/tiff_util.cc.o.d -o CMakeFiles/ost_io.dir/img/tiff_util.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.cc [ 54%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_structure_analysis.cc [ 54%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_contact_overlap.cc [ 54%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_accessibility.cc [ 54%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_entity.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_entity.cc.o -MF CMakeFiles/_ost_gfx.dir/export_entity.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_entity.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_entity.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/complex:44, from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:51:40: warning: 'int32' is deprecated [-Wdeprecated-declarations] 51 | class complexint32:public std::complex{ | ^~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:24: /usr/include/i386-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:61:40: warning: 'int16' is deprecated [-Wdeprecated-declarations] 61 | class complexint16:public std::complex{ | ^~~~~ /usr/include/i386-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:71:39: warning: 'int8' is deprecated [-Wdeprecated-declarations] 71 | class complexint8:public std::complex{ | ^~~~ /usr/include/i386-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:105:114: warning: 'uint16' is deprecated [-Wdeprecated-declarations] 105 | void do_tiff_read(tdata_t buf,unsigned int rps, unsigned int width, IST* is,unsigned int& current_row, uint16 spp) | ^ /usr/include/i386-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 54%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_surface.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_surface.cc.o -MF CMakeFiles/_ost_gfx.dir/export_surface.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_surface.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_surface.cc [ 54%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primitives.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primitives.cc.o -MF CMakeFiles/_ost_gfx.dir/export_primitives.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_primitives.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_primitives.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_trajectory_analysis.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_structure_analysis.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/trajectory_analysis.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_trajectory_analysis.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_accessibility.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/structure_analysis.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_structure_analysis.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 54%] Linking CXX shared library ../../../stage/lib/libost_io.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_io.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_io.so.2.3 -o ../../../stage/lib/libost_io.so.2.3.1 CMakeFiles/ost_io.dir/io_manager.cc.o CMakeFiles/ost_io.dir/convert.cc.o CMakeFiles/ost_io.dir/io_utils.cc.o CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o 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CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o CMakeFiles/ost_io.dir/img/image_format.cc.o CMakeFiles/ost_io.dir/img/tiff_util.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libtiff.so /usr/lib/i386-linux-gnu/libpng.so /usr/lib/i386-linux-gnu/libz.so ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/i386-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img.so.2.3.1 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so /usr/lib/i386-linux-gnu/libboost_program_options.so /usr/lib/i386-linux-gnu/libboost_thread.so /usr/lib/i386-linux-gnu/libboost_chrono.so /usr/lib/i386-linux-gnu/libboost_date_time.so /usr/lib/i386-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_contact_overlap.cc:1: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/accessibility.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_accessibility.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/contact_overlap.hh:6, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_contact_overlap.cc:4: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_entity.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/contact_overlap.hh:8: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_io.so.2.3.1 ../../../stage/lib/libost_io.so.2.3 ../../../stage/lib/libost_io.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 54%] Built target ost_io make -f modules/conop/src/CMakeFiles/chemdict_tool.dir/build.make modules/conop/src/CMakeFiles/chemdict_tool.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/conop/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src/CMakeFiles/chemdict_tool.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/conop/src/CMakeFiles/chemdict_tool.dir/build.make modules/conop/src/CMakeFiles/chemdict_tool.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 54%] Building CXX object modules/conop/src/CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/src/CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o -MF CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o.d -o CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/src/chemdict_tool.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_entity.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_primitives.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_surface.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/primitives.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_primitives.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 54%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_sec_structure.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/surface.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/surface.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_surface.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/chemdict_tool.cc:32: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/conop/src/chemdict_tool.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 54%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primlist.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primlist.cc.o -MF CMakeFiles/_ost_gfx.dir/export_primlist.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_primlist.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_primlist.cc [ 54%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_non_standard.cc [ 54%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_sec_structure.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_sec_structure.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_primlist.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/prim_list.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_primlist.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_non_standard.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 54%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o -MF CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_scene_observer.cc [ 54%] Linking CXX executable ../../../stage/bin/chemdict_tool cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/chemdict_tool.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o -o ../../../stage/bin/chemdict_tool -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../stage/lib/libost_io.so.2.3.1 ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/i386-linux-gnu/libsqlite3.so /usr/lib/i386-linux-gnu/libboost_program_options.so /usr/lib/i386-linux-gnu/libboost_thread.so /usr/lib/i386-linux-gnu/libboost_chrono.so /usr/lib/i386-linux-gnu/libboost_date_time.so /usr/lib/i386-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libtiff.so /usr/lib/i386-linux-gnu/libpng.so /usr/lib/i386-linux-gnu/libz.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 54%] Built target chemdict_tool make -f modules/gui/src/CMakeFiles/ost_gui.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 55%] Generating tools/moc_tool_options_win.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp_parameters [ 55%] Generating data_viewer/moc_argand.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp_parameters In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_non_standard.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 55%] Generating data_viewer/moc_data_viewer.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp_parameters [ 55%] Generating data_viewer/moc_data_viewer_panel_base.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp_parameters [ 55%] Generating data_viewer/moc_fft_panel.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp_parameters [ 55%] Generating data_viewer/moc_info_panel.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp_parameters [ 55%] Generating data_viewer/moc_null_overlay.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_null_overlay.cpp_parameters [ 55%] Generating data_viewer/moc_overlay_base.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_overlay_base.cpp_parameters [ 55%] Generating data_viewer/moc_overlay_manager_gui.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_overlay_manager_gui.cpp_parameters [ 55%] Generating data_viewer/moc_pointlist_overlay_base.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp_parameters In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 55%] Generating messages/moc_log_reader.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/messages && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/messages/moc_log_reader.cpp_parameters [ 55%] Generating messages/moc_message_box_widget.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/messages && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/messages/moc_message_box_widget.cpp_parameters [ 55%] Generating messages/moc_message_widget.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/messages && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/messages/moc_message_widget.cpp_parameters [ 55%] Generating moc_dock_widget.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_dock_widget.cpp_parameters [ 55%] Generating moc_file_browser.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_file_browser.cpp_parameters [ 55%] Generating moc_file_type_dialog.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp_parameters [ 55%] Generating moc_file_viewer.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_file_viewer.cpp_parameters [ 55%] Generating moc_gl_canvas.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_gl_canvas.cpp_parameters [ 55%] Generating moc_gl_win.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_gl_win.cpp_parameters [ 55%] Generating moc_gosty_app.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_gosty_app.cpp_parameters [ 55%] Generating moc_main.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_main.cpp_parameters [ 55%] Generating moc_main_area.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_main_area.cpp_parameters [ 55%] Generating moc_main_window.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_main_window.cpp_parameters [ 55%] Generating moc_perspective.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_perspective.cpp_parameters [ 56%] Generating moc_scene_menu.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_scene_menu.cpp_parameters In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/molck.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 56%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_render_options.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_render_options.cc.o -MF CMakeFiles/_ost_gfx.dir/export_render_options.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_render_options.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_render_options.cc [ 56%] Generating moc_scene_selection.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_scene_selection.cpp_parameters [ 56%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_membrane.cc [ 56%] Generating moc_widget.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_widget.cpp_parameters [ 56%] Generating moc_widget_geom_handler.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_widget_geom_handler.cpp_parameters [ 58%] Generating moc_widget_pool.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_widget_pool.cpp_parameters [ 58%] Generating panels/moc_bottom_bar.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_bottom_bar.cpp_parameters [ 58%] Generating panels/moc_button_bar.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_button_bar.cpp_parameters [ 58%] Generating panels/moc_button_box.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_button_box.cpp_parameters [ 58%] Generating panels/moc_drop_box.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp_parameters [ 58%] Generating panels/moc_event_button.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_event_button.cpp_parameters [ 59%] Generating panels/moc_panel_bar.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_panel_bar.cpp_parameters [ 59%] Generating panels/moc_panel_bar_widget_holder.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_panel_bar_widget_holder.cpp_parameters [ 59%] Generating panels/moc_panel_manager.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_panel_manager.cpp_parameters [ 59%] Generating panels/moc_panel_widget_container.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_panel_widget_container.cpp_parameters [ 59%] Generating panels/moc_side_bar.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_side_bar.cpp_parameters [ 59%] Generating panels/moc_splitter_panel_bar.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_splitter_panel_bar.cpp_parameters [ 59%] Generating panels/moc_tabbed_panel_bar.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_tabbed_panel_bar.cpp_parameters [ 59%] Generating python_shell/moc_completer_base.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_completer_base.cpp_parameters [ 59%] Generating python_shell/moc_gutter.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_gutter.cpp_parameters [ 59%] Generating python_shell/moc_main_thread_runner.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_main_thread_runner.cpp_parameters [ 59%] Generating python_shell/moc_output_redirector.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_output_redirector.cpp_parameters [ 59%] Generating python_shell/moc_path_completer.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_path_completer.cpp_parameters [ 59%] Generating python_shell/moc_python_completer.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_python_completer.cpp_parameters [ 59%] Generating python_shell/moc_python_interpreter.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp_parameters [ 60%] Generating python_shell/moc_python_interpreter_worker.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter_worker.cpp_parameters [ 60%] Generating python_shell/moc_python_namespace_tree_model.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_python_namespace_tree_model.cpp_parameters [ 60%] Generating python_shell/moc_python_shell.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_python_shell.cpp_parameters [ 60%] Generating python_shell/moc_python_shell_widget.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp_parameters [ 60%] Generating python_shell/moc_state.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_state.cpp_parameters [ 60%] Generating python_shell/moc_state_machine.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_state_machine.cpp_parameters [ 60%] Generating python_shell/moc_text_logger.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp_parameters [ 60%] Generating python_shell/moc_transition.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_transition.cpp_parameters [ 60%] Generating python_shell/moc_transition_guard.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_transition_guard.cpp_parameters [ 62%] Generating scene_win/moc_context_menu.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp_parameters [ 62%] Generating scene_win/moc_current_selection_node.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp_parameters [ 62%] Generating scene_win/moc_custom_part_node.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp_parameters In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_scene_observer.cc:1: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 62%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_alg_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -MF CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o.d -o CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_entity_to_density.cc [ 62%] Generating scene_win/moc_entity_node.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp_parameters [ 62%] Generating scene_win/moc_entity_part_node.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp_parameters In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_render_options.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 62%] Generating scene_win/moc_gfx_scene_node.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_gfx_scene_node.cpp_parameters [ 62%] Generating scene_win/moc_label_node.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_label_node.cpp_parameters [ 62%] Generating scene_win/moc_render_mode_node.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp_parameters [ 62%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color.cc.o -MF CMakeFiles/_ost_gfx.dir/export_color.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_color.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_color.cc [ 62%] Generating scene_win/moc_render_modes_node.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp_parameters [ 62%] Generating scene_win/moc_root_node.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_root_node.cpp_parameters [ 63%] Generating scene_win/moc_scene_node.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_scene_node.cpp_parameters [ 63%] Generating scene_win/moc_scene_win.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp_parameters In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_membrane.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 63%] Generating scene_win/moc_scene_win_model.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp_parameters In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/find_membrane.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_membrane.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 63%] Generating sequence_viewer/moc_align_properties_painter.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp_parameters [ 64%] Generating sequence_viewer/moc_alignment_view_object.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp_parameters [ 64%] Generating sequence_viewer/moc_background_painter.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp_parameters [ 64%] Generating sequence_viewer/moc_base_row.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp_parameters [ 64%] Generating sequence_viewer/moc_base_view_object.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp_parameters [ 64%] Generating sequence_viewer/moc_conservation_painter.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp_parameters [ 64%] Generating sequence_viewer/moc_painter.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp_parameters In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_entity_to_density.cc:23: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 64%] Generating sequence_viewer/moc_secstr_row.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp_parameters [ 64%] Generating sequence_viewer/moc_seq_secstr_painter.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp_parameters [ 65%] Generating sequence_viewer/moc_seq_selection_painter.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp_parameters [ 65%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gradient.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gradient.cc.o -MF CMakeFiles/_ost_gfx.dir/export_gradient.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_gradient.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_gradient.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/entity_to_density.hh:4, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/export_entity_to_density.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 65%] Generating sequence_viewer/moc_seq_text_painter.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp_parameters [ 65%] Generating sequence_viewer/moc_sequence_delegate.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp_parameters [ 65%] Generating sequence_viewer/moc_sequence_model.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp_parameters [ 65%] Generating sequence_viewer/moc_sequence_row.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp_parameters [ 65%] Generating sequence_viewer/moc_sequence_search_bar.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp_parameters [ 65%] Generating sequence_viewer/moc_sequence_table_view.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp_parameters [ 65%] Generating sequence_viewer/moc_sequence_view_object.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp_parameters [ 65%] Generating sequence_viewer/moc_sequence_viewer.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp_parameters [ 65%] Generating sequence_viewer/moc_tick_painter.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp_parameters [ 65%] Generating sequence_viewer/moc_title_row.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp_parameters [ 65%] Generating tools/moc_measure_tool.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp_parameters [ 65%] Generating tools/moc_tool.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool.cpp_parameters In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_color.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ [ 65%] Generating tools/moc_tool_bar.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_bar.cpp_parameters /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 65%] Generating tools/moc_tool_manager.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_manager.cpp_parameters [ 65%] Generating tools/moc_tool_option.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_option.cpp_parameters [ 65%] Generating tools/moc_tool_option_group.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_option_group.cpp_parameters [ 65%] Generating tools/moc_tool_options.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_options.cpp_parameters [ 65%] Generating tools/moc_tool_options_widget.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_options_widget.cpp_parameters [ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o -MF CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_color_ops.cc [ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o -MF CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_glwin_base.cc [ 67%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_exporter.cc.o In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_color.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_exporter.cc.o -MF CMakeFiles/_ost_gfx.dir/export_exporter.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_exporter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_exporter.cc /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gui/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/CMakeFiles/ost_gui.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gui/src/CMakeFiles/ost_gui.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 68%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_file_browser.cpp [ 69%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/mol/alg/_ost_mol_alg.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../../stage/lib/python3.11/dist-packages/ost/mol/alg/_ost_mol_alg.so CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so /usr/lib/i386-linux-gnu/libboost_program_options.so /usr/lib/i386-linux-gnu/libboost_thread.so /usr/lib/i386-linux-gnu/libboost_chrono.so /usr/lib/i386-linux-gnu/libboost_date_time.so /usr/lib/i386-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libsqlite3.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/views.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./views.pyc\",\"views.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/superpose.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./superpose.pyc\",\"superpose.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/qsscoring.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./qsscoring.pyc\",\"qsscoring.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/trajectory_analysis.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./trajectory_analysis.pyc\",\"trajectory_analysis.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/structure_analysis.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./structure_analysis.pyc\",\"structure_analysis.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/helix_kinks.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./helix_kinks.pyc\",\"helix_kinks.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/mol/alg/pymod/hbond.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./hbond.pyc\",\"hbond.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 69%] Built target _ost_mol_alg make -f modules/io/tests/CMakeFiles/test_mae_standalone.dir/build.make modules/io/tests/CMakeFiles/test_mae_standalone.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/io/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests/CMakeFiles/test_mae_standalone.dir/DependInfo.cmake --color= In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_gradient.cc:24: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/io/tests/CMakeFiles/test_mae_standalone.dir/build.make modules/io/tests/CMakeFiles/test_mae_standalone.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 69%] Building CXX object modules/io/tests/CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o -MF CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o.d -o CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_mae_standalone.cc [ 69%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o -MF CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_bitmap.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gradient.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_gradient.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/../../../../modules/gui/src/file_browser.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_file_browser.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_file_browser.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_exporter.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_color_ops.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_glwin_base.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_mae_standalone.cc:2: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_mae_standalone.cc:1: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_color_ops.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 69%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_map.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gfx_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_map.cc.o -MF CMakeFiles/_ost_gfx.dir/export_map.cc.o.d -o CMakeFiles/_ost_gfx.dir/export_map.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_map.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_bitmap.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_file_viewer.cpp [ 69%] Linking CXX executable ../../../stage/bin/test_mae_standalone cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/test_mae_standalone.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o -o ../../../stage/bin/test_mae_standalone -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_regex.so ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/i386-linux-gnu/libsqlite3.so /usr/lib/i386-linux-gnu/libboost_program_options.so /usr/lib/i386-linux-gnu/libboost_thread.so /usr/lib/i386-linux-gnu/libboost_chrono.so /usr/lib/i386-linux-gnu/libboost_date_time.so /usr/lib/i386-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libtiff.so /usr/lib/i386-linux-gnu/libpng.so /usr/lib/i386-linux-gnu/libz.so [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_gl_canvas.cpp make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 69%] Built target test_mae_standalone make -f modules/mol/alg/src/CMakeFiles/lddt.dir/build.make modules/mol/alg/src/CMakeFiles/lddt.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src/CMakeFiles/lddt.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/mol/alg/src/CMakeFiles/lddt.dir/build.make modules/mol/alg/src/CMakeFiles/lddt.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 69%] Building CXX object modules/mol/alg/src/CMakeFiles/lddt.dir/lddt.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/src/CMakeFiles/lddt.dir/lddt.cc.o -MF CMakeFiles/lddt.dir/lddt.cc.o.d -o CMakeFiles/lddt.dir/lddt.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/lddt.cc make -f tools/molck/CMakeFiles/molck.dir/build.make tools/molck/CMakeFiles/molck.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/tools/molck /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/tools/molck /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/tools/molck/CMakeFiles/molck.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f tools/molck/CMakeFiles/molck.dir/build.make tools/molck/CMakeFiles/molck.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 69%] Building CXX object tools/molck/CMakeFiles/molck.dir/main.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/tools/molck && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT tools/molck/CMakeFiles/molck.dir/main.cc.o -MF CMakeFiles/molck.dir/main.cc.o.d -o CMakeFiles/molck.dir/main.cc.o -c /build/reproducible-path/openstructure-2.3.1/tools/molck/main.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/../../../../modules/gui/src/file_type_dialog.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/../../../../modules/gui/src/gl_canvas.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_gl_canvas.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/QPoint:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_gl_win.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o -MF CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_scene_menu.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o -MF CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_gosty_app.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/reproducible-path/openstructure-2.3.1/tools/molck/main.cc:8: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/program_options/errors.hpp:12, from /usr/include/boost/program_options/options_description.hpp:12, from /usr/include/boost/program_options.hpp:15, from /build/reproducible-path/openstructure-2.3.1/tools/molck/main.cc:2: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/export_map.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/iomanip:40, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:19: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.3.1/tools/molck/main.cc:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:31: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:39: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_main.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_area.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_area.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main_area.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main_area.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_main_area.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_perspective.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_perspective.cpp.o -MF CMakeFiles/ost_gui.dir/moc_perspective.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_perspective.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_perspective.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o -MF CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_dock_widget.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/../../../../modules/gui/src/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_gosty_app.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_window.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_window.cpp.o -MF CMakeFiles/ost_gui.dir/moc_main_window.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_main_window.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_main_window.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_dock_widget.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/../../../../modules/gui/src/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/i386-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qdockwidget.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QDockWidget:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/../../../../modules/gui/src/dock_widget.hh:31: /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_main.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o -MF CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_scene_selection.cpp [ 70%] Linking CXX executable ../../stage/bin/molck cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/tools/molck && /usr/bin/cmake -E cmake_link_script CMakeFiles/molck.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/molck.dir/main.cc.o -o ../../stage/bin/molck -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../stage/lib/libost_io.so.2.3.1 ../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_program_options.so /usr/lib/i386-linux-gnu/libboost_thread.so /usr/lib/i386-linux-gnu/libboost_chrono.so /usr/lib/i386-linux-gnu/libboost_date_time.so /usr/lib/i386-linux-gnu/libboost_atomic.so ../../stage/lib/libost_seq_alg.so.2.3.1 ../../stage/lib/libost_conop.so.2.3.1 ../../stage/lib/libost_db.so.2.3.1 /usr/lib/i386-linux-gnu/libsqlite3.so ../../stage/lib/libost_seq.so.2.3.1 ../../stage/lib/libost_mol.so.2.3.1 ../../stage/lib/libost_img_alg.so.2.3.1 ../../stage/lib/libost_img.so.2.3.1 ../../stage/lib/libost_info.so.2.3.1 ../../stage/lib/libost_base.so.2.3.1 ../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libtiff.so /usr/lib/i386-linux-gnu/libpng.so /usr/lib/i386-linux-gnu/libz.so [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_widget.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget_geom_handler.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_widget_geom_handler.cpp make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 70%] Built target molck make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/io/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod/CMakeFiles/_ost_io.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 70%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/wrap_io.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/wrap_io.cc.o -MF CMakeFiles/_ost_io.dir/wrap_io.cc.o.d -o CMakeFiles/_ost_io.dir/wrap_io.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/wrap_io.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_main_window.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/../../../../modules/gui/src/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/i386-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QMainWindow:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/../../../../modules/gui/src/main_window.hh:35: /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh: In instantiation of 'ost::gui::WidgetStateSaver::~WidgetStateSaver() [with BASE = QMainWindow]': /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:40:25: required from here /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh:323:8: warning: the address of 'ost::gui::WidgetStateSaver::' will never be NULL [-Waddress] 323 | if(dynamic_cast(this)){ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh:263:7: note: 'ost::gui::WidgetStateSaver::' declared here 263 | class WidgetStateSaver: public BASE | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/../../../../modules/gui/src/scene_selection.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_scene_selection.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_scene_selection.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 70%] Linking CXX executable ../../../../stage/bin/lddt cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/lddt.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/lddt.dir/lddt.cc.o -o ../../../../stage/bin/lddt -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_program_options.so /usr/lib/i386-linux-gnu/libboost_thread.so /usr/lib/i386-linux-gnu/libboost_chrono.so /usr/lib/i386-linux-gnu/libboost_date_time.so /usr/lib/i386-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libsqlite3.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libtiff.so /usr/lib/i386-linux-gnu/libpng.so /usr/lib/i386-linux-gnu/libz.so [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o -MF CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o.d -o CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_widget_pool.cpp make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 70%] Built target lddt [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/messages/moc_message_widget.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/messages/moc_message_box_widget.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o -MF CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o.d -o CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/messages/moc_log_reader.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/align_properties_painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/background_painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/gfx/_ost_gfx.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/gradients.xml /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/scene/gradients.xml cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_gfx.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/gfx/_ost_gfx.so CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o CMakeFiles/_ost_gfx.dir/export_scene.cc.o CMakeFiles/_ost_gfx.dir/export_gfx_node.cc.o CMakeFiles/_ost_gfx.dir/export_symmetry_node.cc.o CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o CMakeFiles/_ost_gfx.dir/export_entity.cc.o CMakeFiles/_ost_gfx.dir/export_surface.cc.o CMakeFiles/_ost_gfx.dir/export_primitives.cc.o CMakeFiles/_ost_gfx.dir/export_primlist.cc.o CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o CMakeFiles/_ost_gfx.dir/export_render_options.cc.o CMakeFiles/_ost_gfx.dir/export_color.cc.o CMakeFiles/_ost_gfx.dir/export_gradient.cc.o CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o CMakeFiles/_ost_gfx.dir/export_exporter.cc.o CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o CMakeFiles/_ost_gfx.dir/export_map.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../stage/lib/libost_gfx.so.2.3.1 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/i386-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so /usr/lib/i386-linux-gnu/libOpenGL.so /usr/lib/i386-linux-gnu/libGLX.so /usr/lib/i386-linux-gnu/libGLU.so /usr/lib/i386-linux-gnu/libpng.so /usr/lib/i386-linux-gnu/libz.so In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/wrap_io.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/conservation_painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/wrap_io.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./__init__.pyc\",\"__init__.py\",doraise=True)" In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/secstr_row.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod/py_gfx_obj.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./py_gfx_obj.pyc\",\"py_gfx_obj.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Built target _ost_gfx [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_selection_painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_secstr_painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_text_painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 72%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_row.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_search_bar.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_table_view.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_title_row.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_viewer.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/tick_painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_alignment_view_object.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_view_object.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/title_row.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_view_object.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_main_thread_runner.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_main_thread_runner.cpp [ 73%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_pdb_io.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_pdb_io.cc.o -MF CMakeFiles/_ost_io.dir/export_pdb_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_pdb_io.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_view_object.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_completer_base.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_completer_base.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/alignment_view_object.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_gutter.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_output_redirector.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_path_completer.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_path_completer.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_completer.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_python_completer.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:32: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_interpreter_worker.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter_worker.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_namespace_tree_model.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_python_namespace_tree_model.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_shell.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_python_shell.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_python_shell_widget.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_text_logger.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_state_machine.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_state.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_transition.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o -MF CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o.d -o CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_transition_guard.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter_worker.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_button_bar.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_bar.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_panel_bar.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_shell_widget.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/../../../../../modules/gui/src/panels/drop_box.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_panel_manager.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_bottom_bar.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_bottom_bar.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/transition.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_transition.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_button_box.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_button_box.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/transition_guard.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/python_shell/moc_transition_guard.cpp:10: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_event_button.cpp [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_panel_widget_container.cpp [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_panel_bar_widget_holder.cpp [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_side_bar.cpp [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_splitter_panel_bar.cpp [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o -MF CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/panels/moc_tabbed_panel_bar.cpp [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp [ 77%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o -MF CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_gfx_scene_node.cpp [ 77%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_label_node.cpp [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/current_selection_node.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/custom_part_node.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/context_menu.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_root_node.cpp [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_scene_node.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/entity_part_node.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/entity_node.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o -MF CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o.d -o CMakeFiles/ost_gui.dir/scene_win/moc_scene_win_model.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_mode_node.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool.cpp In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_mode_node.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_modes_node.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_option_group.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/scene_win.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_options.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_options.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/scene_win_model.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/QPoint:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_bar.cpp [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_option.cpp [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_manager.cpp [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_options_widget.cpp [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o -MF CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o.d -o CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/tool_manager.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_manager.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/QPoint:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_argand.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_argand.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_argand.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_argand.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/tool_bar.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_bar.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/QPoint:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_info_panel.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/measure_tool.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/QPoint:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_manager_gui.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_overlay_manager_gui.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/tool_options_win.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/QPoint:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/measure_tool.hh:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/argand.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/info_panel.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data_observer.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/fft_panel.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_data_viewer_panel_base.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_null_overlay.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_null_overlay.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_overlay_base.cpp [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o -MF CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o.d -o CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/thin_splitter.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/thin_splitter.cc.o -MF CMakeFiles/ost_gui.dir/thin_splitter.cc.o.d -o CMakeFiles/ost_gui.dir/thin_splitter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/thin_splitter.cc [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/perspective.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/perspective.cc.o -MF CMakeFiles/ost_gui.dir/perspective.cc.o.d -o CMakeFiles/ost_gui.dir/perspective.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/perspective.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer.hh:37: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/i386-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QMainWindow:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main_window.hh:35: /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_registry.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_registry.cc.o -MF CMakeFiles/ost_gui.dir/widget_registry.cc.o.d -o CMakeFiles/ost_gui.dir/widget_registry.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/widget_registry.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/pointlist_overlay_base.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp:10: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp:9: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_browser.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_browser.cc.o -MF CMakeFiles/ost_gui.dir/file_browser.cc.o.d -o CMakeFiles/ost_gui.dir/file_browser.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_browser.cc [ 81%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_type_dialog.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_type_dialog.cc.o -MF CMakeFiles/ost_gui.dir/file_type_dialog.cc.o.d -o CMakeFiles/ost_gui.dir/file_type_dialog.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_type_dialog.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_viewer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_viewer.cc.o -MF CMakeFiles/ost_gui.dir/file_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/file_viewer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_viewer.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main.cc.o -MF CMakeFiles/ost_gui.dir/main.cc.o.d -o CMakeFiles/ost_gui.dir/main.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/main.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/file_browser.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/perspective.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/platform.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/perspective.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_canvas.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gl_canvas.cc.o -MF CMakeFiles/ost_gui.dir/gl_canvas.cc.o.d -o CMakeFiles/ost_gui.dir/gl_canvas.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gl_canvas.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/dock_widget.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/dock_widget.cc.o -MF CMakeFiles/ost_gui.dir/dock_widget.cc.o.d -o CMakeFiles/ost_gui.dir/dock_widget.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/dock_widget.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_type_dialog.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_type_dialog.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_type_dialog.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main_window.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/main_window.cc.o -MF CMakeFiles/ost_gui.dir/main_window.cc.o.d -o CMakeFiles/ost_gui.dir/main_window.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/main_window.cc In file included from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/dock_widget.cc:25: /build/reproducible-path/openstructure-2.3.1/modules/gui/src/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/i386-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qdockwidget.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QDockWidget:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/dock_widget.hh:31: /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_win.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/gl_win.cc.o -MF CMakeFiles/ost_gui.dir/gl_win.cc.o.d -o CMakeFiles/ost_gui.dir/gl_win.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gl_win.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_menu.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_menu.cc.o -MF CMakeFiles/ost_gui.dir/scene_menu.cc.o.d -o CMakeFiles/ost_gui.dir/scene_menu.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_menu.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_browser.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/main_window.cc:25: /build/reproducible-path/openstructure-2.3.1/modules/gui/src/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/i386-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QMainWindow:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/main_window.hh:35: /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/main_window.cc:26: /build/reproducible-path/openstructure-2.3.1/modules/gui/src/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); | ^ /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/dock_widget.hh: In member function 'void ost::gui::MainWindow::AddDockWidget(QWidget*, const QString&, bool, int)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); | ^ /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/main_window.cc:71:33: warning: 'QVariant qVariantFromValue(const T&) [with T = QDockWidget*]' is deprecated: Use QVariant::fromValue() instead. [-Wdeprecated-declarations] 71 | act->setData(qVariantFromValue((QDockWidget*)dock)); | ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtWidgets/qaction.h:47, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qmenu.h:47, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QMenu:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/main_window.hh:36: /usr/include/i386-linux-gnu/qt5/QtCore/qvariant.h:530:17: note: declared here 530 | inline QVariant qVariantFromValue(const T &t) | ^~~~~~~~~~~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget.cc.o -MF CMakeFiles/ost_gui.dir/widget.cc.o.d -o CMakeFiles/ost_gui.dir/widget.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/widget.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/main.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_browser.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/file_loader.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_browser.cc:34: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gl_canvas.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/QPoint:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_browser.cc: In constructor 'ost::gui::FileBrowser::FileBrowser(QWidget*)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_browser.cc:62:13: warning: 'QDirModel::QDirModel(QObject*)' is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] 62 | model_(new QDirModel), | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtWidgets/QDirModel:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_browser.cc:53: /usr/include/i386-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); | ^~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_browser.cc: In constructor 'ost::gui::FileBrowser::FileBrowser(const QString&, QWidget*)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_browser.cc:102:13: warning: 'QDirModel::QDirModel(QObject*)' is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] 102 | model_(new QDirModel), | ^~~~~~~~~ /usr/include/i386-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); | ^~~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/admin.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/admin.cc.o -MF CMakeFiles/ost_gui.dir/admin.cc.o.d -o CMakeFiles/ost_gui.dir/admin.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/admin.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/file_loader.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/main.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/glwin_base.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gl_canvas.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_pool.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_pool.cc.o -MF CMakeFiles/ost_gui.dir/widget_pool.cc.o.d -o CMakeFiles/ost_gui.dir/widget_pool.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/widget_pool.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/file_loader.hh:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_widget.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_widget.cc.o -MF CMakeFiles/ost_gui.dir/messages/message_widget.cc.o.d -o CMakeFiles/ost_gui.dir/messages/message_widget.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/messages/message_widget.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/smart_ptr/weak_ptr.hpp:17, from /usr/include/boost/smart_ptr/enable_shared_from_this.hpp:16, from /usr/include/boost/enable_shared_from_this.hpp:16, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_node.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:29: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/main.cc:31: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/i386-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/i386-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/i386-linux-gnu/qt5/QtCore/QTime:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/main.cc: In static member function 'static QSize ost::gui::GostyMainWindow::GetDefaultSize()': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/main.cc:59:64: warning: 'const QRect QDesktopWidget::availableGeometry(int) const' is deprecated: Use QGuiApplication::screens() [-Wdeprecated-declarations] 59 | QRect desktop_geom=QApplication::desktop()->availableGeometry(); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/i386-linux-gnu/qt5/QtWidgets/QDesktopWidget:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/main.cc:35: /usr/include/i386-linux-gnu/qt5/QtWidgets/qdesktopwidget.h:88:67: note: declared here 88 | QT_DEPRECATED_X("Use QGuiApplication::screens()") const QRect availableGeometry(int screen = -1) const; | ^~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gl_canvas.cc: In member function 'void ost::gui::GLCanvas::HandleMouseMoveEvent(QMouseEvent*)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:373:32: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 373 | if (event->buttons() & Qt::MidButton) { | ^~~~~~~~~ /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:399:37: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 399 | } else if (event->buttons() & Qt::MidButton) { | ^~~~~~~~~ /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gl_canvas.cc: In member function 'virtual void ost::gui::GLCanvas::wheelEvent(QWheelEvent*)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:488:50: warning: 'int QWheelEvent::delta() const' is deprecated: Use angleDelta() [-Wdeprecated-declarations] 488 | 0.2*static_cast(-event->delta())); | ~~~~~~~~~~~~^~ In file included from /usr/include/i386-linux-gnu/qt5/QtGui/QMouseEvent:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:25: /usr/include/i386-linux-gnu/qt5/QtGui/qevent.h:219:16: note: declared here 219 | inline int delta() const { return qt4D; } | ^~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/widget_state_saver.hh: In instantiation of 'ost::gui::WidgetStateSaver::~WidgetStateSaver() [with BASE = QMainWindow]': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/main.cc:69:69: required from here /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:323:8: warning: the address of 'ost::gui::WidgetStateSaver::' will never be NULL [-Waddress] 323 | if(dynamic_cast(this)){ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:263:7: note: 'ost::gui::WidgetStateSaver::' declared here 263 | class WidgetStateSaver: public BASE | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_menu.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/widget_state_saver.hh: In instantiation of 'void ost::gui::WidgetStateSaver::set_state_() [with BASE = QMainWindow]': /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:286:5: required from 'ost::gui::WidgetStateSaver::WidgetStateSaver(const QString&, QPoint, QSize, QWidget*) [with BASE = QMainWindow]' /build/reproducible-path/openstructure-2.3.1/modules/gui/src/main.cc:69:69: required from here /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:305:10: warning: the address of 'ost::gui::WidgetStateSaver::' will never be NULL [-Waddress] 305 | if(dynamic_cast(this)){ | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:263:7: note: 'ost::gui::WidgetStateSaver::' declared here 263 | class WidgetStateSaver: public BASE | ^~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gl_win.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o -MF CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o.d -o CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/view_op.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_menu.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/log_reader.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/messages/log_reader.cc.o -MF CMakeFiles/ost_gui.dir/messages/log_reader.cc.o.d -o CMakeFiles/ost_gui.dir/messages/log_reader.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/messages/log_reader.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/align_properties_painter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/base_row.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gl_win.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gl_canvas.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gl_win.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/i386-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/i386-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/i386-linux-gnu/qt5/QtCore/QTime:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/messages/message_widget.cc:23: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.cc:23: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_secstr_painter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_selection_painter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/seq_text_painter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.cc [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_row.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/chain_view.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.cc:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.cc:31: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.cc /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.cc: In member function 'virtual int ost::gui::SequenceTableView::sizeHintForColumn(int) const': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.cc:480:35: warning: 'int QFontMetrics::width(QChar) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 480 | return this->fontMetrics().width('W'); | ~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtGui/qpainter.h:59, from /usr/include/i386-linux-gnu/qt5/QtGui/QPainter:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:35: /usr/include/i386-linux-gnu/qt5/QtGui/qfontmetrics.h:110:9: note: declared here 110 | int width(QChar) const; | ^~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/alignment_view_object.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/chain_view.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:23: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/algorithm:60, from /usr/include/i386-linux-gnu/qt5/QtCore/qglobal.h:142, from /usr/include/i386-linux-gnu/qt5/QtCore/QtCore:4, from /usr/include/i386-linux-gnu/qt5/QtGui/QtGuiDepends:3, from /usr/include/i386-linux-gnu/qt5/QtGui/QtGui:3, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.cc [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o -MF CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o.d -o CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_region.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_region.hh:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc: In member function 'void ost::gui::SequenceViewer::MouseWheelEvent(QWheelEvent*)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:298:27: warning: 'int QWheelEvent::delta() const' is deprecated: Use angleDelta() [-Wdeprecated-declarations] 298 | int delta = event->delta(); | ~~~~~~~~~~~~^~ In file included from /usr/include/i386-linux-gnu/qt5/QtGui/QWheelEvent:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:42: /usr/include/i386-linux-gnu/qt5/QtGui/qevent.h:219:16: note: declared here 219 | inline int delta() const { return qt4D; } | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:299:25: warning: 'Qt::Orientation QWheelEvent::orientation() const' is deprecated: Use angleDelta() [-Wdeprecated-declarations] 299 | if (event->orientation() == Qt::Vertical) { | ~~~~~~~~~~~~~~~~~~^~ /usr/include/i386-linux-gnu/qt5/QtGui/qevent.h:222:28: note: declared here 222 | inline Qt::Orientation orientation() const { return qt4O; } | ^~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_state_saver.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_state_saver.cc.o -MF CMakeFiles/ost_gui.dir/widget_state_saver.cc.o.d -o CMakeFiles/ost_gui.dir/widget_state_saver.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/widget_state_saver.cc [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_selection.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_selection.cc.o -MF CMakeFiles/ost_gui.dir/scene_selection.cc.o.d -o CMakeFiles/ost_gui.dir/scene_selection.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_selection.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.cc:32: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o -MF CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o.d -o CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/widget_geom_handler.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gosty_app.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_loader.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/file_loader.cc.o -MF CMakeFiles/ost_gui.dir/file_loader.cc.o.d -o CMakeFiles/ost_gui.dir/file_loader.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_loader.cc [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_bar.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/button_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/button_bar.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/button_bar.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gosty_app.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/i386-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/i386-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/i386-linux-gnu/qt5/QtCore/QTime:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/drop_box.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/drop_box.cc.o -MF CMakeFiles/ost_gui.dir/panels/drop_box.cc.o.d -o CMakeFiles/ost_gui.dir/panels/drop_box.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/drop_box.cc [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/panel_bar.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gosty_app.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gosty_app.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gosty_app.cc:31: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/i386-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/qstring.h:49: /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_selection.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 86%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/bottom_bar.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_box.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_box.cc.o -MF CMakeFiles/ost_gui.dir/panels/button_box.cc.o.d -o CMakeFiles/ost_gui.dir/panels/button_box.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/button_box.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/drop_box.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/drop_box.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /usr/include/boost/ptr_container/ptr_vector.hpp:19, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/view_op.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_selection.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_selection.cc:34: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/i386-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/qstring.h:49, from /usr/include/i386-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/i386-linux-gnu/qt5/QtCore/QTime:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/event_button.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/event_button.cc.o -MF CMakeFiles/ost_gui.dir/panels/event_button.cc.o.d -o CMakeFiles/ost_gui.dir/panels/event_button.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/event_button.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_loader.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/panel_manager.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/panel_bar.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/panel_widget_container.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o -MF CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o.d -o CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/panel_bar_widget_holder.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_loader.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_loader.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/event_button.cc: In member function 'virtual void ost::gui::EventButton::mouseMoveEvent(QMouseEvent*)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/event_button.cc:50:15: warning: 'Qt::DropAction QDrag::start(Qt::DropActions)' is deprecated: Use QDrag::exec() instead [-Wdeprecated-declarations] 50 | drag->start(Qt::MoveAction); | ~~~~~~~~~~~^~~~~~~~~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtGui/QDrag:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/event_button.cc:22: /usr/include/i386-linux-gnu/qt5/QtGui/qdrag.h:79:20: note: declared here 79 | Qt::DropAction start(Qt::DropActions supportedActions = Qt::CopyAction); | ^~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/side_bar.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/side_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/side_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/side_bar.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/side_bar.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_loader.hh:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/splitter_panel_bar.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/splitter_panel_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/splitter_panel_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/splitter_panel_bar.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/splitter_panel_bar.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/drop_box.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/panel_bar.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/file_loader.cc:51: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/i386-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/qstring.h:49, from /usr/include/i386-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/i386-linux-gnu/qt5/QtCore/QTime:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o -MF CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o.d -o CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/tabbed_panel_bar.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_option_group.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_option_group.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_options.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_options.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_options.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_option.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_option.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_option.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_option.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_manager.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/panel_bar_widget_holder.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_manager.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_manager.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/QPoint:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o -MF CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o.d -o CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/mouse_event.cc In file included from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool.cc:19: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/QPoint:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/tabbed_panel_bar.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/manipulator.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/manipulator.cc.o -MF CMakeFiles/ost_gui.dir/tools/manipulator.cc.o.d -o CMakeFiles/ost_gui.dir/tools/manipulator.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/manipulator.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_options_widget.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o -MF CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o.d -o CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_bar.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/selection_tool.cc [ 88%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_omf_io.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_omf_io.cc.o -MF CMakeFiles/_ost_io.dir/export_omf_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_omf_io.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/export_omf_io.cc In file included from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/mouse_event.cc:19: /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/QPoint:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh:24: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/measure_tool.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/gutter.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/selection_tool.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/selection_tool.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/QPoint:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/selection_tool.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/i386-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/i386-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/i386-linux-gnu/qt5/QtCore/QTime:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/measure_tool.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/QPoint:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_bar.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/completer_base.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/manipulator.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/export_omf_io.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_bar.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_bar.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/i386-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/i386-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/i386-linux-gnu/qt5/QtCore/QTime:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc: In member function 'void ost::gui::OutputRedirector::Write(const String&)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:42:22: warning: 'int QTime::elapsed() const' is deprecated: Use QElapsedTimer instead [-Wdeprecated-declarations] 42 | if(timer_.elapsed()>1000){ | ~~~~~~~~~~~~~~^~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/QTime:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:25: /usr/include/i386-linux-gnu/qt5/QtCore/qdatetime.h:237:54: note: declared here 237 | QT_DEPRECATED_X("Use QElapsedTimer instead") int elapsed() const; | ^~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:46:21: warning: 'int QTime::restart()' is deprecated: Use QElapsedTimer instead [-Wdeprecated-declarations] 46 | timer_.restart(); | ~~~~~~~~~~~~~~^~ /usr/include/i386-linux-gnu/qt5/QtCore/qdatetime.h:236:54: note: declared here 236 | QT_DEPRECATED_X("Use QElapsedTimer instead") int restart(); | ^~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:52:17: warning: 'void QTime::start()' is deprecated: Use QElapsedTimer instead [-Wdeprecated-declarations] 52 | timer_.start(); | ~~~~~~~~~~~~^~ /usr/include/i386-linux-gnu/qt5/QtCore/qdatetime.h:235:55: note: declared here 235 | QT_DEPRECATED_X("Use QElapsedTimer instead") void start(); | ^~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/omf.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/export_omf_io.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mmcif_info.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/omf.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/manipulator.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/gutter.cc:22: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/manipulator.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/manipulator.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/i386-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/i386-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/i386-linux-gnu/qt5/QtCore/QTime:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/path_completer.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.cc: In constructor 'ost::gui::OstDirModel::OstDirModel(QObject*)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.cc:31:18: warning: 'QDirModel::QDirModel(QObject*)' is deprecated: Use QFileSystemModel [-Wdeprecated-declarations] 31 | QDirModel(parent) | ^ In file included from /usr/include/i386-linux-gnu/qt5/QtWidgets/QDirModel:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.cc:23: /usr/include/i386-linux-gnu/qt5/QtWidgets/qdirmodel.h:73:67: note: declared here 73 | QT_DEPRECATED_VERSION_X_5_15("Use QFileSystemModel") explicit QDirModel(QObject *parent = nullptr); | ^~~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_context_parser.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_completer.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_model.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_item.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_text_document_layout.cc [ 91%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_map_io.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_io_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/io/pymod/CMakeFiles/_ost_io.dir/export_map_io.cc.o -MF CMakeFiles/_ost_io.dir/export_map_io.cc.o.d -o CMakeFiles/_ost_io.dir/export_map_io.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/export_map_io.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_tokenizer.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.cc:24: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_model.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_item.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_item.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_syntax_highlighter.cc /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_model.cc: In member function 'virtual Qt::ItemFlags ost::gui::PythonNamespaceTreeModel::flags(const QModelIndex&) const': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_model.cc:110:12: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::ItemFlag; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 110 | return 0; | ^ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/i386-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/qstring.h:49, from /usr/include/i386-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/i386-linux-gnu/qt5/QtCore/QTime:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:33: /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/shell_history.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/string_literal_positions.cc /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc: In constructor 'ost::gui::PythonShellWidget::PythonShellWidget(QWidget*)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc:79:34: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 79 | setTabStopWidth(2*metrics.width(" ")); | ~~~~~~~~~~~~~^~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtWidgets/qwidget.h:50, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qframe.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qabstractscrollarea.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qtextedit.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qplaintextedit.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QPlainTextEdit:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:34: /usr/include/i386-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc:79:18: warning: 'void QPlainTextEdit::setTabStopWidth(int)' is deprecated [-Wdeprecated-declarations] 79 | setTabStopWidth(2*metrics.width(" ")); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/qt5/QtWidgets/qplaintextedit.h:179:24: note: declared here 179 | QT_DEPRECATED void setTabStopWidth(int width); | ^~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc: In member function 'void ost::gui::PythonShellWidget::SetTabWidth(int)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc:537:43: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 537 | setTabStopWidth(tab_width_*metrics.width(" ")); | ~~~~~~~~~~~~~^~~~~ /usr/include/i386-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc:537:18: warning: 'void QPlainTextEdit::setTabStopWidth(int)' is deprecated [-Wdeprecated-declarations] 537 | setTabStopWidth(tab_width_*metrics.width(" ")); | ~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/qt5/QtWidgets/qplaintextedit.h:179:24: note: declared here 179 | QT_DEPRECATED void setTabStopWidth(int width); | ^~~~~~~~~~~~~~~ [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/state_machine.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/export_map_io.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/state.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/state.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/state.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/map.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_handler.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/io/pymod/export_map_io.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/transition.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/transition.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/transition.cc [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o -MF CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o.d -o CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.cc [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.cc [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.cc [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/pointer_cast.hpp:52, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/transition.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/state.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_node.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/transition.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.cc:21: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/label_node.cc [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.cc [ 92%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.cc [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.cc [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/label_node.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/label_node.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/label_node.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_node_fw.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/root_node.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o -MF CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o.d -o CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.cc [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/map_tool.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/tools/map_tool.cc.o -MF CMakeFiles/ost_gui.dir/tools/map_tool.cc.o.d -o CMakeFiles/ost_gui.dir/tools/map_tool.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/argand.cc [ 93%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/io/_ost_io.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_io.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/io/_ost_io.so CMakeFiles/_ost_io.dir/wrap_io.cc.o CMakeFiles/_ost_io.dir/export_pdb_io.cc.o CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o CMakeFiles/_ost_io.dir/export_omf_io.cc.o CMakeFiles/_ost_io.dir/export_map_io.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/i386-linux-gnu/libsqlite3.so /usr/lib/i386-linux-gnu/libboost_program_options.so /usr/lib/i386-linux-gnu/libboost_thread.so /usr/lib/i386-linux-gnu/libboost_chrono.so /usr/lib/i386-linux-gnu/libboost_date_time.so /usr/lib/i386-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libtiff.so /usr/lib/i386-linux-gnu/libpng.so /usr/lib/i386-linux-gnu/libz.so In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/argand.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/argand.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/argand.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/io/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/io/pymod/remote.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./remote.pyc\",\"remote.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/io/pymod/repository.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./repository.pyc\",\"repository.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 93%] Built target _ost_io [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/root_node.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/root_node.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/root_node.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.hh:27: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc:23: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/map_slab.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/platform.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.cc [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.cc: In member function 'virtual QMimeData* ost::gui::SceneWinModel::mimeData(const QModelIndexList&) const': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.cc:231:26: warning: 'QByteArray& QByteArray::append(const QString&)' is deprecated: Use QString's toUtf8(), toLatin1() or toLocal8Bit() [-Wdeprecated-declarations] 231 | encoded_data.append(text); | ~~~~~~~~~~~~~~~~~~~^~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qobject.h:47, from /usr/include/i386-linux-gnu/qt5/QtCore/QObject:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.hh:34: /usr/include/i386-linux-gnu/qt5/QtCore/qstring.h:1511:20: note: declared here 1511 | inline QByteArray &QByteArray::append(const QString &s) | ^~~~~~~~~~ [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_selection.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/map_slab.hh:26: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc: In member function 'void ost::gui::SceneWin::RowsInserted(const QModelIndex&, int, int)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc:117:31: warning: 'QModelIndex QModelIndex::child(int, int) const' is deprecated: Use QAbstractItemModel::index [-Wdeprecated-declarations] 117 | model->select(parent.child(start,0),QItemSelectionModel::ClearAndSelect|QItemSelectionModel::Rows); | ~~~~~~~~~~~~^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/QModelIndex:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc:26: /usr/include/i386-linux-gnu/qt5/QtCore/qabstractitemmodel.h:455:20: note: declared here 455 | inline QModelIndex QModelIndex::child(int arow, int acolumn) const | ^~~~~~~~~~~ [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/map_tool.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/i386-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/i386-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/i386-linux-gnu/qt5/QtCore/QTime:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc:25: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/norm.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/normalizer_impl.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:26: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.cc /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc: In member function 'virtual void ost::img::gui::DataViewerPanelBase::paintEvent(QPaintEvent*)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:440:56: warning: 'static bool QPixmapCache::find(const QString&, QPixmap&)' is deprecated: Use bool find(const QString &, QPixmap *) instead [-Wdeprecated-declarations] 440 | if (update_raster_image_ || ( !QPixmapCache::find(cache_key, pm))) { | ~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtGui/QPixmapCache:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:40: /usr/include/i386-linux-gnu/qt5/QtGui/qpixmapcache.h:81:17: note: declared here 81 | static bool find(const QString &key, QPixmap &pixmap); | ^~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc: In member function 'virtual void ost::img::gui::DataViewerPanelBase::mouseMoveEvent(QMouseEvent*)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:602:38: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 602 | } else if((event->buttons() == Qt::MidButton) && HasSelection()) { | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qobjectdefs.h:48, from /usr/include/i386-linux-gnu/qt5/QtGui/qwindowdefs.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qwidget.h:44, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QWidget:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:46, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:34: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc: In member function 'virtual void ost::img::gui::DataViewerPanelBase::wheelEvent(QWheelEvent*)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:613:18: warning: 'int QWheelEvent::delta() const' is deprecated: Use angleDelta() [-Wdeprecated-declarations] 613 | if(event->delta()>0) { | ~~~~~~~~~~~~^~ In file included from /usr/include/i386-linux-gnu/qt5/QtGui/QResizeEvent:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:36: /usr/include/i386-linux-gnu/qt5/QtGui/qevent.h:219:16: note: declared here 219 | inline int delta() const { return qt4D; } | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc: In member function 'void ost::img::gui::DataViewerPanelBase::draw_pixel_values(QPainter&)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:1074:49: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 1074 | int string_w=painter.fontMetrics().width(value_string); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtWidgets/qwidget.h:50: /usr/include/i386-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:1090:49: warning: 'int QFontMetrics::width(const QString&, int) const' is deprecated: Use QFontMetrics::horizontalAdvance [-Wdeprecated-declarations] 1090 | int string_w=painter.fontMetrics().width(value_string); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~ /usr/include/i386-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/algorithm:60, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.cc [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/norm.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:36: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:37: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/dock_widget.hh:38:77: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 38 | DockWidget(const QString& title, QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/i386-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/qstring.h:49, from /usr/include/i386-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/i386-linux-gnu/qt5/QtCore/QTime:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:41: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/fft.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/fft.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc: In constructor 'ost::img::gui::DataViewer::DataViewer(QWidget*, const ost::img::ImageHandle&, const QString&)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:75:14: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 75 | lastmouse_() | ^ /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc: In member function 'void ost::img::gui::DataViewer::build(const ost::img::ImageHandle&)': /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:315:54: warning: 'const QRect QDesktopWidget::availableGeometry(int) const' is deprecated: Use QGuiApplication::screens() [-Wdeprecated-declarations] 315 | resize(QApplication::desktop()->availableGeometry().adjusted(20,20,-20,-20).size()); | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~ In file included from /usr/include/i386-linux-gnu/qt5/QtWidgets/QDesktopWidget:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:53: /usr/include/i386-linux-gnu/qt5/QtWidgets/qdesktopwidget.h:88:67: note: declared here 88 | QT_DEPRECATED_X("Use QGuiApplication::screens()") const QRect availableGeometry(int screen = -1) const; | ^~~~~~~~~~~~~~~~~ [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/null_overlay.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /usr/include/boost/format.hpp:17, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/circle_mask.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/mask_visitor.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:30: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.cc [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_gui.cc [ 96%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.cc [ 96%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay_base.cc [ 96%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.cc [ 96%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DOST_MODULE_OST_GUI -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o -MF CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o.d -o CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/message.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay_base.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/stat.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.cc:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.cc:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 96%] Linking CXX shared library ../../../stage/lib/libost_gui.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gui.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -Wl,-soname,libost_gui.so.2.3 -o ../../../stage/lib/libost_gui.so.2.3.1 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CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o CMakeFiles/ost_gui.dir/python_shell/gutter.cc.o CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o CMakeFiles/ost_gui.dir/python_shell/path_completer.cc.o CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_model.cc.o CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o CMakeFiles/ost_gui.dir/python_shell/state.cc.o CMakeFiles/ost_gui.dir/python_shell/transition.cc.o CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o CMakeFiles/ost_gui.dir/scene_win/current_selection_node.cc.o CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o CMakeFiles/ost_gui.dir/scene_win/gfx_scene_node.cc.o CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o CMakeFiles/ost_gui.dir/scene_win/render_modes_node.cc.o CMakeFiles/ost_gui.dir/scene_win/root_node.cc.o CMakeFiles/ost_gui.dir/scene_win/scene_win.cc.o CMakeFiles/ost_gui.dir/scene_win/scene_win_model.cc.o CMakeFiles/ost_gui.dir/tools/map_tool.cc.o CMakeFiles/ost_gui.dir/data_viewer/argand.cc.o CMakeFiles/ost_gui.dir/data_viewer/data_viewer.cc.o CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o CMakeFiles/ost_gui.dir/data_viewer/drawing_functions.cc.o CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o CMakeFiles/ost_gui.dir/data_viewer/info_panel.cc.o CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o CMakeFiles/ost_gui.dir/data_viewer/overlay_base.cc.o CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o CMakeFiles/ost_gui.dir/data_viewer/overlay_manager_gui.cc.o CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay.cc.o CMakeFiles/ost_gui.dir/data_viewer/pointlist_overlay_base.cc.o CMakeFiles/ost_gui.dir/data_viewer/strategies.cc.o CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../stage/lib/libost_gfx.so.2.3.1 ../../../stage/lib/libost_io.so.2.3.1 ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_seq_alg.so.2.3.1 /usr/lib/i386-linux-gnu/libOpenGL.so /usr/lib/i386-linux-gnu/libGLX.so /usr/lib/i386-linux-gnu/libGLU.so /usr/lib/i386-linux-gnu/libboost_program_options.so /usr/lib/i386-linux-gnu/libboost_thread.so /usr/lib/i386-linux-gnu/libboost_chrono.so /usr/lib/i386-linux-gnu/libboost_date_time.so /usr/lib/i386-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/i386-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libtiff.so /usr/lib/i386-linux-gnu/libpng.so /usr/lib/i386-linux-gnu/libz.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E cmake_symlink_library ../../../stage/lib/libost_gui.so.2.3.1 ../../../stage/lib/libost_gui.so.2.3 ../../../stage/lib/libost_gui.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 96%] Built target ost_gui make -f modules/gui/src/CMakeFiles/gosty.dir/build.make modules/gui/src/CMakeFiles/gosty.dir/depend make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 96%] Generating qrc_dngr.cpp [ 96%] Generating moc_gosty.cpp cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/rcc --name dngr --output /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/qrc_dngr.cpp /build/reproducible-path/openstructure-2.3.1/modules/gui/src/dngr.qrc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_gosty.cpp_parameters make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod/CMakeFiles/_ost_gui.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 96%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o [ 96%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_message_widget.cc.o [ 96%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_win.cc.o [ 96%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/wrap_gui.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o -MF CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o.d -o CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_alignment_view.cc [ 96%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_tool.cc.o [ 96%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gosty.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/wrap_gui.cc.o -MF CMakeFiles/_ost_gui.dir/wrap_gui.cc.o.d -o CMakeFiles/_ost_gui.dir/wrap_gui.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/wrap_gui.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_message_widget.cc.o -MF CMakeFiles/_ost_gui.dir/export_message_widget.cc.o.d -o CMakeFiles/_ost_gui.dir/export_message_widget.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_message_widget.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_win.cc.o -MF CMakeFiles/_ost_gui.dir/export_gl_win.cc.o.d -o CMakeFiles/_ost_gui.dir/export_gl_win.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_gl_win.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gosty.cc.o -MF CMakeFiles/_ost_gui.dir/export_gosty.cc.o.d -o CMakeFiles/_ost_gui.dir/export_gosty.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_tool.cc.o -MF CMakeFiles/_ost_gui.dir/export_tool.cc.o.d -o CMakeFiles/_ost_gui.dir/export_tool.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_tool.cc [ 97%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_py_shell.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gui/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/CMakeFiles/gosty.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_py_shell.cc.o -MF CMakeFiles/_ost_gui.dir/export_py_shell.cc.o.d -o CMakeFiles/_ost_gui.dir/export_py_shell.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_py_shell.cc make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gui/src/CMakeFiles/gosty.dir/build.make modules/gui/src/CMakeFiles/gosty.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 98%] Building CXX object modules/gui/src/CMakeFiles/gosty.dir/gosty.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gui/src/CMakeFiles/gosty.dir/gosty.cc.o -MF CMakeFiles/gosty.dir/gosty.cc.o.d -o CMakeFiles/gosty.dir/gosty.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gosty.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_tool.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_gl_win.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_alignment_view.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gui/src/gosty.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_alignment_view.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/wrap_gui.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_tool.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/QPoint:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_py_shell.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_message_widget.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_win.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_win.cc.o -MF CMakeFiles/_ost_gui.dir/export_scene_win.cc.o.d -o CMakeFiles/_ost_gui.dir/export_scene_win.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_scene_win.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o -MF CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o.d -o CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_sequence_viewer.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_perspective.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_perspective.cc.o -MF CMakeFiles/_ost_gui.dir/export_perspective.cc.o.d -o CMakeFiles/_ost_gui.dir/export_perspective.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_perspective.cc [ 98%] Building CXX object modules/gui/src/CMakeFiles/gosty.dir/moc_gosty.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gui/src/CMakeFiles/gosty.dir/moc_gosty.cpp.o -MF CMakeFiles/gosty.dir/moc_gosty.cpp.o.d -o CMakeFiles/gosty.dir/moc_gosty.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/moc_gosty.cpp In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/i386-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/i386-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/i386-linux-gnu/qt5/QtCore/QTime:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:24: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:32: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o -MF CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o.d -o CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_sip_handler.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o -MF CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o.d -o CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_scene_selection.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:41, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:38: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/i386-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/qstring.h:49: /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ [ 98%] Building CXX object modules/gui/src/CMakeFiles/gosty.dir/qrc_dngr.cpp.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gui/src/CMakeFiles/gosty.dir/qrc_dngr.cpp.o -MF CMakeFiles/gosty.dir/qrc_dngr.cpp.o.d -o CMakeFiles/gosty.dir/qrc_dngr.cpp.o -c /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/qrc_dngr.cpp [ 98%] Linking CXX executable ../../../stage/lib/openstructure/libexec/gosty cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/gosty.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/gosty.dir/gosty.cc.o CMakeFiles/gosty.dir/moc_gosty.cpp.o CMakeFiles/gosty.dir/qrc_dngr.cpp.o -o ../../../stage/lib/openstructure/libexec/gosty -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../stage/lib/libost_gui.so.2.3.1 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../stage/lib/libost_gfx.so.2.3.1 /usr/lib/i386-linux-gnu/libOpenGL.so /usr/lib/i386-linux-gnu/libGLX.so /usr/lib/i386-linux-gnu/libGLU.so ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/i386-linux-gnu/libtiff.so /usr/lib/i386-linux-gnu/libpng.so /usr/lib/i386-linux-gnu/libz.so ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/i386-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so /usr/lib/i386-linux-gnu/libboost_program_options.so /usr/lib/i386-linux-gnu/libboost_thread.so /usr/lib/i386-linux-gnu/libboost_chrono.so /usr/lib/i386-linux-gnu/libboost_date_time.so /usr/lib/i386-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_regex.so make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 98%] Built target gosty [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_main_area.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_main_area.cc.o -MF CMakeFiles/_ost_gui.dir/export_main_area.cc.o.d -o CMakeFiles/_ost_gui.dir/export_main_area.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_main_area.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_scene_win.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_scene_win.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_perspective.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_sequence_viewer.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_sequence_viewer.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_sip_handler.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_panels.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_panels.cc.o -MF CMakeFiles/_ost_gui.dir/export_panels.cc.o.d -o CMakeFiles/_ost_gui.dir/export_panels.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_panels.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_scene_selection.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_main_area.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o -MF CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o.d -o CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_menu_bar.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_selection.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_scene_selection.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_loader.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_loader.cc.o -MF CMakeFiles/_ost_gui.dir/export_file_loader.cc.o.d -o CMakeFiles/_ost_gui.dir/export_file_loader.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_file_loader.cc [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o -MF CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o.d -o CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_file_viewer.cc [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_widget.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_widget.cc.o -MF CMakeFiles/_ost_gui.dir/export_widget.cc.o.d -o CMakeFiles/_ost_gui.dir/export_widget.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_widget.cc [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o -MF CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o.d -o CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_gl_canvas.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_panels.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o -MF CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o.d -o CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_menu_bar.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o -MF CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o.d -o CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_data_viewer.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_file_viewer.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_file_loader.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_widget.cc:20: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/file_loader.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_file_loader.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_gl_canvas.cc:19: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/file_loader.hh:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay.cc.o -MF CMakeFiles/_ost_gui.dir/export_overlay.cc.o.d -o CMakeFiles/_ost_gui.dir/export_overlay.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_overlay.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/gl_canvas.hh:23, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_gl_canvas.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:37:22: warning: 'Qt::MidButton' is deprecated: MidButton is deprecated. Use MiddleButton instead [-Wdeprecated-declarations] 37 | MiddleButton=Qt::MidButton | ^~~~~~~~~ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/i386-linux-gnu/qt5/QtCore/QPoint:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/i386-linux-gnu/qt5/QtCore/qnamespace.h:132:9: note: declared here 132 | MidButton Q_DECL_ENUMERATOR_DEPRECATED_X("MidButton is deprecated. Use MiddleButton instead") = MiddleButton, | ^~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/sip_handler.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.cc:26: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_gui_EXPORTS -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -fPIC -MD -MT modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o -MF CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o.d -o CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_overlay_manager.cc In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_data_viewer.cc:25: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:35: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:41: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/i386-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qwidget.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QWidget:1, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/sip_handler.hh:24: /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:33, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_data_viewer.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main_window.hh:46:55: warning: 'constexpr QFlags::QFlags(Zero) [with Enum = Qt::WindowType; Zero = int QFlags::Private::*]' is deprecated: Use default constructor instead [-Wdeprecated-declarations] 46 | MainWindow(QWidget* parent=0, Qt::WindowFlags flags=0); | ^ In file included from /usr/include/i386-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/i386-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, from /usr/include/i386-linux-gnu/qt5/QtWidgets/QMainWindow:1, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/main_window.hh:35: /usr/include/i386-linux-gnu/qt5/QtCore/qflags.h:123:80: note: declared here 123 | QT_DEPRECATED_X("Use default constructor instead") Q_DECL_CONSTEXPR inline QFlags(Zero) noexcept : i(0) {} | ^~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_overlay.cc:26: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/smart_ptr/detail/sp_thread_sleep.hpp:22, from /usr/include/boost/smart_ptr/detail/yield_k.hpp:23, from /usr/include/boost/smart_ptr/detail/spinlock_gcc_atomic.hpp:14, from /usr/include/boost/smart_ptr/detail/spinlock.hpp:42, from /usr/include/boost/smart_ptr/detail/spinlock_pool.hpp:25, from /usr/include/boost/smart_ptr/shared_ptr.hpp:29, from /usr/include/boost/shared_ptr.hpp:17, from /usr/include/boost/python/converter/shared_ptr_to_python.hpp:12, from /usr/include/boost/python/converter/arg_to_python.hpp:15, from /usr/include/boost/python/call.hpp:15, from /usr/include/boost/python/object_core.hpp:14, from /usr/include/boost/python/args.hpp:22, from /usr/include/boost/python.hpp:11, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_overlay_manager.cc:16: /usr/include/boost/bind.hpp:36:1: note: '#pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.' 36 | BOOST_PRAGMA_MESSAGE( | ^~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point_list.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/export_overlay.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /usr/include/c++/12/math.h:36, from /usr/include/python3.11/pyport.h:218, from /usr/include/python3.11/Python.h:38, from /usr/include/boost/python/detail/wrap_python.hpp:178, from /usr/include/boost/python/detail/prefix.hpp:13, from /usr/include/boost/python/args.hpp:8: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [100%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/gui/_ost_gui.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/presets.xml /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/scene/presets.xml cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/icons/color_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/scene/icons/color_icon.png cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/icons/preset_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/scene/icons/preset_icon.png cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/icons/render_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/scene/icons/render_icon.png cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/icons/tool_icon.png /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/share/openstructure/scene/icons/tool_icon.png cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_gui.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro -shared -o ../../../stage/lib/python3.11/dist-packages/ost/gui/_ost_gui.so CMakeFiles/_ost_gui.dir/wrap_gui.cc.o CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o CMakeFiles/_ost_gui.dir/export_message_widget.cc.o CMakeFiles/_ost_gui.dir/export_gl_win.cc.o CMakeFiles/_ost_gui.dir/export_tool.cc.o CMakeFiles/_ost_gui.dir/export_py_shell.cc.o CMakeFiles/_ost_gui.dir/export_gosty.cc.o CMakeFiles/_ost_gui.dir/export_scene_win.cc.o CMakeFiles/_ost_gui.dir/export_sequence_viewer.cc.o CMakeFiles/_ost_gui.dir/export_perspective.cc.o CMakeFiles/_ost_gui.dir/export_sip_handler.cc.o CMakeFiles/_ost_gui.dir/export_scene_selection.cc.o CMakeFiles/_ost_gui.dir/export_main_area.cc.o CMakeFiles/_ost_gui.dir/export_panels.cc.o CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o CMakeFiles/_ost_gui.dir/export_file_loader.cc.o CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o CMakeFiles/_ost_gui.dir/export_widget.cc.o CMakeFiles/_ost_gui.dir/export_gl_canvas.cc.o CMakeFiles/_ost_gui.dir/data_viewer_proxy.cc.o CMakeFiles/_ost_gui.dir/export_data_viewer.cc.o CMakeFiles/_ost_gui.dir/export_overlay.cc.o CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib: ../../../stage/lib/libost_gui.so.2.3.1 /usr/lib/i386-linux-gnu/libpython3.11.so /usr/lib/i386-linux-gnu/libboost_python311.so ../../../stage/lib/libost_gfx.so.2.3.1 /usr/lib/i386-linux-gnu/libOpenGL.so /usr/lib/i386-linux-gnu/libGLX.so /usr/lib/i386-linux-gnu/libGLU.so ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/i386-linux-gnu/libtiff.so /usr/lib/i386-linux-gnu/libpng.so /usr/lib/i386-linux-gnu/libz.so ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/i386-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so /usr/lib/i386-linux-gnu/libboost_program_options.so /usr/lib/i386-linux-gnu/libboost_thread.so /usr/lib/i386-linux-gnu/libboost_chrono.so /usr/lib/i386-linux-gnu/libboost_date_time.so /usr/lib/i386-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_regex.so cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/__init__.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/color_options_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_options_widget.pyc\",\"color_options_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/color_select_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_select_widget.pyc\",\"color_select_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/combo_options_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/combo_options_widget.pyc\",\"combo_options_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/cpk_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/cpk_widget.pyc\",\"cpk_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/custom_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/custom_widget.pyc\",\"custom_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/gradient_editor_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_editor_widget.pyc\",\"gradient_editor_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/gradient_info_handler.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_info_handler.pyc\",\"gradient_info_handler.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/gradient_list_model.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_list_model.pyc\",\"gradient_list_model.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/gradient_preset_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_preset_widget.pyc\",\"gradient_preset_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/hsc_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/hsc_widget.pyc\",\"hsc_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/immutable_gradient_info_handler.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_gradient_info_handler.pyc\",\"immutable_gradient_info_handler.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/immutable_preset_info_handler.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_preset_info_handler.pyc\",\"immutable_preset_info_handler.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/init_inspector.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/init_inspector.pyc\",\"init_inspector.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/inspector_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/inspector_widget.pyc\",\"inspector_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/map_level_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/map_level_widget.pyc\",\"map_level_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/preset.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset.pyc\",\"preset.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/remote.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/remote.pyc\",\"remote.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/preset_editor_list_model.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_list_model.pyc\",\"preset_editor_list_model.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/preset_editor_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_widget.pyc\",\"preset_editor_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/preset_info_handler.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_info_handler.pyc\",\"preset_info_handler.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/preset_list_model.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_list_model.pyc\",\"preset_list_model.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/preset_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_widget.pyc\",\"preset_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/render_mode_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_mode_widget.pyc\",\"render_mode_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/render_op.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_op.pyc\",\"render_op.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/render_options_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_options_widget.pyc\",\"render_options_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/scene_observer_impl.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_observer_impl.pyc\",\"scene_observer_impl.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/scene_selection_helper.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_selection_helper.pyc\",\"scene_selection_helper.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/simple_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/simple_widget.pyc\",\"simple_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/sline_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/sline_widget.pyc\",\"sline_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/toolbar_options_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/toolbar_options_widget.pyc\",\"toolbar_options_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/trace_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/trace_widget.pyc\",\"trace_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/tube_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/tube_widget.pyc\",\"tube_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/uniform_color_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/uniform_color_widget.pyc\",\"uniform_color_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/visibility_op.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/visibility_op.pyc\",\"visibility_op.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/line_trace_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/line_trace_widget.pyc\",\"line_trace_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/wireframe_widget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/wireframe_widget.pyc\",\"wireframe_widget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/scene/query_editor.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/query_editor.pyc\",\"query_editor.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/dng/__init__.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/dng/termuse.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/termuse.pyc\",\"termuse.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/dng/superpositiondialog.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/superpositiondialog.pyc\",\"superpositiondialog.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/dng/init.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/init.pyc\",\"init.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/dng/menu.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/menu.pyc\",\"menu.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/__init__.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/init_context_menu.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_context_menu.pyc\",\"init_context_menu.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/init_menubar.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_menubar.pyc\",\"init_menubar.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/init_spacenav.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_spacenav.pyc\",\"init_spacenav.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/init_splash.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_splash.pyc\",\"init_splash.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/trajectory_viewer.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./trajectory_viewer.pyc\",\"trajectory_viewer.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/helpwidget.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./helpwidget.pyc\",\"helpwidget.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/table.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./table.pyc\",\"table.py\",doraise=True)" cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/reproducible-path/openstructure-2.3.1/modules/gui/pymod/gosty_startup.py\",\"/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./gosty_startup.pyc\",\"gosty_startup.py\",doraise=True)" make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [100%] Built target _ost_gui make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/depend make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts/CMakeFiles/ost_scripts.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/build make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_config /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/openstructure/libexec/ost_config cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/bin/ost cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different dng /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/bin/dng cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_startup.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/ost_startup.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/scripts/dng_startup.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/dng_startup.py make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [100%] Built target ost_scripts make[2]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' dh_auto_test cd obj-i686-linux-gnu && make -j8 check ARGS\+=--verbose ARGS\+=-j8 make[1]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/openstructure-2.3.1 -B/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 check make[2]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' /usr/bin/cmake -S/build/reproducible-path/openstructure-2.3.1 -B/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/CMakeFiles 94 make -f CMakeFiles/Makefile2 CMakeFiles/check.dir/all make[3]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/depend make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/depend make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/depend make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/depend make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts/CMakeFiles/subst_ost_startup.py.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src/CMakeFiles/create_stage.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts/CMakeFiles/subst_ost_config.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts/CMakeFiles/subst_ost.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts/CMakeFiles/subst_dng.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/build make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/build make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/build make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.3.1/scripts/ost_config.in -DOUT_FILE=ost_config -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.3.1/cmake_support/substitute.cmake make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.3.1/scripts/ost_startup.py.in -DOUT_FILE=ost_startup.py -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.3.1/cmake_support/substitute.cmake make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.3.1/scripts/dng.in -DOUT_FILE=dng -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.3.1/cmake_support/substitute.cmake make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/reproducible-path/openstructure-2.3.1/scripts/ost.in -DOUT_FILE=ost -DBUILD_TYPE=Release -DPython_EXECUTABLE=/usr/bin/python3 -DPython_VERSION=3.11.2 -DLIBDIR=lib -DLIBEXEC_PATH=lib/openstructure/libexec -DPYTHON_MODULE_PATH=python3.11/dist-packages/ -P /build/reproducible-path/openstructure-2.3.1/cmake_support/substitute.cmake cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/bin make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/openstructure/libexec [ 0%] Built target subst_ost_config [ 0%] Built target subst_ost_startup.py [ 0%] Built target subst_ost [ 0%] Built target subst_dng cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/tests make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 0%] Built target create_stage make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/depend make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/depend make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/depend make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/DependInfo.cmake --color= make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/geom/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src/CMakeFiles/ost_geom_headers.dir/DependInfo.cmake --color= make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/config /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/config /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/config/CMakeFiles/ost_config_headers.dir/DependInfo.cmake --color= make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src/CMakeFiles/ost_base_headers.dir/DependInfo.cmake --color= make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/info/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src/CMakeFiles/ost_info_headers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/conop/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src/CMakeFiles/ost_conop_headers.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/build make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/build make -f modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/build make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/export_helper/generic_property_def.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/export_helper/generic_property_def.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/config/./base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./base.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/info/src/CMakeFiles/ost_info_headers.dir/build.make modules/info/src/CMakeFiles/ost_info_headers.dir/build make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/pointer_iterator.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/build make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/export_helper/vector.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/export_helper/vector.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./alignment_opts.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./alignment_opts.hh make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./conop.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./conop.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/export_helper/pair_to_tuple_conv.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/config/./config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/atom_group.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/atom_group.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_error.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_error.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./def.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./def.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./clip_alignment.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./processor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./processor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/export_helper/vec_to_list_conv.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/export_helper/vec_to_list_conv.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/config/./dllexport.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./dllexport.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/atom_prop.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/atom_prop.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./exc.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./exc.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./conservation.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./conservation.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./amino_acids.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./amino_acids.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/test_utils/compare_files.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/test_utils/compare_files.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/config/./version.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./version.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./contact_prediction_score.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./contact_prediction_score.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./geom.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./geom.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./diag.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./diag.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./generic_property.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./generic_property.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./contact_weight_matrix.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./mat.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./mat.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./model_check.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./model_check.hh [ 0%] Built target ost_config_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_iterator.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./integrity_error.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./integrity_error.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_group.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_group.hh make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/db/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src/CMakeFiles/ost_db_headers.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./distance_map.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./distance_map.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./heuristic.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./heuristic.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./mat2.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./mat2.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./sequence_list.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./sequence_list.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_item.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_item.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./entropy.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./entropy.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./invalid_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./invalid_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./compound.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./compound.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./mat3.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./mat3.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/db/src/./sqlite_wrap.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/./sqlite_wrap.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./sequence_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./sequence_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./global_align.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./global_align.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./compound_lib.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./compound_lib.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./mat4.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./mat4.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/db/src/./sqlite_conv.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/./sqlite_conv.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./ins_del.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./ins_del.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./ptr_observer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./ptr_observer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./alignment_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./alignment_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vec.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vec.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./local_align.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./local_align.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_path.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_path.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/db/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./rule_based.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./rule_based.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vec2.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vec2.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_set.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_set.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/db/src/./linear_indexer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/./linear_indexer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./minimal_compound_lib.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./log.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./log.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/dihedral.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./sequence_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./sequence_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./merge_pairwise_alignments.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./merge_pairwise_alignments.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vec3.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vec3.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_visitor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_visitor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/db/src/./binary_container.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/./binary_container.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./compound_lib_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./log_sink.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./log_sink.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./aligned_region.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./aligned_region.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vec4.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vec4.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./info_verbose_visitor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./info_verbose_visitor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/db/src/./extract_data_helper.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/db/./extract_data_helper.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/conop/src/./ring_finder.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/./ring_finder.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/entity_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./profile.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./profile.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./aligned_column.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./aligned_column.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./pair_subst_weight_matrix.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./pair_subst_weight_matrix.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vecmat_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vecmat_op.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/fragment_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./item_type.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./item_type.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./dyn_cast.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./dyn_cast.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./aligned_column_iterator.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./aligned_column_iterator.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./semiglobal_align.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./semiglobal_align.hh [ 0%] Built target ost_conop_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./geom_info_conversion.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./geom_info_conversion.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/fragment_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vecmat2_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend [ 0%] Built target ost_db_headers make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gfx/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/DependInfo.cmake --color= make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_headers.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./stdint.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./stdint.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./sequence_identity.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./sequence_identity.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./invalid_sequence.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./invalid_sequence.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vecmat3_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/info/src/./item_type_cast.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/info/./item_type_cast.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/query_ast.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/query_ast.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./sequence_similarity.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./sequence_similarity.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./views_from_sequences.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./stdint_msc.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./stdint_msc.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vecmat4_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/query_ast_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src/./profile_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/./profile_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./range.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./range.hh [ 0%] Built target ost_info_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./subst_weight_matrix.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./subst_weight_matrix.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/dispatch.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/dispatch.hh make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/depend cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./circular_iterator.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./circular_iterator.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/query_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./module_config.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./variance_map.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./constants.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./constants.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./anisotropic.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./anisotropic.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh [ 0%] Built target ost_seq_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./units.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./units.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/query_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/query_impl_fw.hh make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gui/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./data/default_contact_weight_matrix.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./default_contact_weight_matrix.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_iso_spec.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./composite.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./composite.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./auto_correlate.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./message.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./message.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./composite2.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./composite2.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/map_octree.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./clear.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./clear.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./platform.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./platform.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/residue_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_base_fw.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./composite3.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./composite3.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./string_ref.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./string_ref.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./data/default_pair_subst_weight_matrix.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_option_group.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./clip_min_max.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./clip_min_max.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/surface_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_def.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./composite_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./composite_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./pod_vector.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./pod_vector.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/surface_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./conjugate.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./conjugate.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_factory.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_bar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/custom_renderer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./composite2_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./composite2_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./convolute.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./convolute.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_frequency_domain.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_frequency_domain.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./fixed_string.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./fixed_string.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/selection_tool.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./composite3_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./composite3_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./correlate.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./correlate.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./tri_matrix.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./tri_matrix.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./cross_correlate.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./cross_correlate.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./hmm_pseudo_counts.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./aligned_cuboid.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./aligned_cuboid.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./atom_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./atom_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./boost_filesystem_helper.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_option.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_option.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./density_slice.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./density_slice.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src/./hmm_score.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./vec_mat_predicates.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./vec_mat_predicates.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_spatial_domain.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./atom_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./atom_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./dft.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./dft.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_manager.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/base/src/./paged_array.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/./paged_array.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./quat.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./quat.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_visitor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./atom_view.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./atom_view.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./fft.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./fft.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh [ 0%] Built target ost_seq_alg_headers make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/io/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src/CMakeFiles/ost_io_headers.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_options_widget.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_options_widget.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./transform.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./transform.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_algorithm.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./bond_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./bond_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/line_trace_renderer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./fftw_helper.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./fftw_helper.hh [ 0%] Built target ost_base_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_visitor_fw.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./point_cloud.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./point_cloud.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/manipulator.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/manipulator.hh make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/build make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./bond_table.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./bond_table.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./fill.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./fill.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/index.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/index.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/star_parser.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/star_parser.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./svd_superpose.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./svd_superpose.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/geom/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/type_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/type_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./chain_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./chain_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./filter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./filter.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/mmcif_info.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./chain_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./chain_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/image_state/value_holder.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/value_holder.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/tools/map_tool.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/tools/map_tool.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./sec_structure_segments.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./fourier_filters.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh [ 0%] Built target ost_geom_headers make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/depend cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/io_profile.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/io_profile.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/bindings/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./algorithm.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./algorithm.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./chain_view.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./chain_view.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./local_dist_diff_test.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./local_dist_diff_test.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./gaussian_gradient_magnitude.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./gaussian_gradient_magnitude.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./circle_mask.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./circle_mask.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/dcd_io.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/dcd_io.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./chain_type.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./chain_type.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/bindings/src/./wrap_tmalign.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/bindings/./wrap_tmalign.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/base_row.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./distance_test_common.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./distance_test_common.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./gaussian.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./gaussian.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./composite_mask.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./composite_mask.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/entity_io_crd_handler.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./chem_class.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./chem_class.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/background_painter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./distance_rmsd_test.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./distance_rmsd_test.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./gaussian_laplacian.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/entity_renderer_fw.hh [ 0%] Built target ost_bindings_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./data_algorithm.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./data_algorithm.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/entity_io_pqr_handler.hh make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/config /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/config /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/config/CMakeFiles/ost_config.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./chem_type.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./chem_type.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/conservation_painter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./superpose_frames.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./highest_peak_search_3d.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./highest_peak_search_3d.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/entity_io_mae_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./data_observer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./data_observer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/tabulated_trig.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/tabulated_trig.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/config/CMakeFiles/ost_config.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./coord_group.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./coord_group.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/painter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./filter_clashes.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./histogram.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./histogram.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./data_types.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./data_types.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/fast_spheres.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh [ 0%] Built target ost_config cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./coord_source.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./coord_source.hh make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/geom/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/src/CMakeFiles/ost_geom.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./construct_cbeta.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./line_iterator.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./line_iterator.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/secstr_row.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/entity_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./data.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./data.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./in_mem_coord_source.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./in_mem_coord_source.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_secstr_painter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./clash_score.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./local_sigma_threshold.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./local_sigma_threshold.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./debug.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./debug.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./coord_frame.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./coord_frame.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/line_render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_selection_painter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/entity_io_pdb_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./trajectory_analysis.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./trajectory_analysis.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./mask_image.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./mask_image.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./dllexport.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./dllexport.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./editor_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./editor_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/custom_render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/custom_render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_text_painter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_writer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/pdb_writer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./structure_analysis.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./structure_analysis.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./extent_iterator.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./extent_iterator.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./negate.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./negate.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./editor_type_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/cpk_render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/cpk_render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_delegate.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/entity_io_sdf_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./extent_mask.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./extent_mask.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./normalizer_factory.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./normalizer_factory.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./mol.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./mol.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_model.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/sdf_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/sdf_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/simple_render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./pdbize.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./pdbize.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./norm.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./norm.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./extent.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./extent.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_row.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./adjacency_bitmap.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./adjacency_bitmap.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/sline_render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/sline_render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./normalizer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./normalizer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image_factory.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image_factory.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_search_bar.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/save_entity.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/save_entity.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/line_trace_render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./norm_linear.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./norm_linear.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_table_view.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./contact_overlap.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./norm_log.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./norm_log.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/load_entity.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/load_entity.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/cartoon_render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/cartoon_render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_observer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_observer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image_handle_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image_handle_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./domain_find.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./norm_od.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./norm_od.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/render_options/trace_render_options.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/surface_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_observer_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/tick_painter.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./similarity_matrix.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./similarity_matrix.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/load_surface.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/load_surface.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./power_spectrum.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./power_spectrum.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_property_mapper.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/title_row.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./accessibility.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./accessibility.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/geom/src/CMakeFiles/ost_geom.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./randomize.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./randomize.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/surface_io_msms_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_view.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_view.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/alignment_view_object.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./sec_struct.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./sec_struct.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image_list.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image_list.hh [ 1%] Built target ost_geom cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/pdb_str.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/pdb_str.hh make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/depend cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_visitor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_visitor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./smooth_mask_image.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./smooth_mask_image.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/src/CMakeFiles/ost_base.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/base_view_object.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./nonstandard.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./nonstandard.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image_state_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image_state_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/uniform_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./entity_visitor_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./stat.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./stat.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./molck.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./molck.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image_state.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image_state.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_view_object.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./stat_accumulator.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./stat_accumulator.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./handle_type_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./handle_type_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./find_membrane.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./find_membrane.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/main_thread_runner.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./image.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./image.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/mol/omf.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/omf.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./stat_min_max.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./stat_min_max.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/entity_view_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src/./entity_to_density.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./ics_editor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./ics_editor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./inverted_mask.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./inverted_mask.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/load_map.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/load_map.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./threshold.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./threshold.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/basic_gradient_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./map.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./map.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./not_connected_error.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./not_connected_error.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/base/src/CMakeFiles/ost_base.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/completer_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/completer_base.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./transcendentals.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./transcendentals.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./mask_base_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./mask_base_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/image_format.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/image_format.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./property_id.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./property_id.hh [ 2%] Built target ost_base [ 2%] Built target ost_mol_alg_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/dir_model.hh make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/depend make -f modules/geom/tests/CMakeFiles/ost_geom_tests.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/geom/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/pymod/CMakeFiles/_ost_geom.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./transform.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./transform.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color_ops/map_handle_color_op.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/geom/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests/CMakeFiles/ost_geom_tests.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./mask_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./mask_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_dx_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./query.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./query.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/gutter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/gutter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./transform_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./transform_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./render_pass.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./render_pass.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./mask_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./mask_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_spi_handler.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/geom/tests/CMakeFiles/ost_geom_tests.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./query_error.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./query_error.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/path_completer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/path_completer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./alg_transform.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./alg_transform.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./mask_visitor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./mask_visitor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./bitmap_io.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh [ 2%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_situs_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_composite3.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_context_parser.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_context_parser.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./query_state.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./query_state.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./alg_mirror.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./alg_mirror.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./collada_exporter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./mask.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./mask.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_completer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_completer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./residue_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./residue_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./alg_shift.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./alg_shift.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_mrc_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./color.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./color.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_shell.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./discrete_shrink.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./discrete_shrink.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./residue_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./residue_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./normalizer_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./normalizer_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_dat_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./entity.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./entity.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_shell_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./transformation_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./residue_prop.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./residue_prop.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./normalizer_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./normalizer_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./entity_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./entity_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_ipl_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./transformations.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./transformations.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_shell_widget.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./residue_view.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./residue_view.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./null_data.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./null_data.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_jpk_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gl_helper.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gl_helper.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./fractional_shift.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./fractional_shift.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./observable.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./observable.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_tokenizer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_tokenizer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./sec_structure.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./sec_structure.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_nanoscope_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./paste_impl.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./paste_impl.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_syntax_highlighter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_syntax_highlighter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./spatial_organizer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./spatial_organizer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_png_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./polar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./polar.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./peak.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./peak.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./surface.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./surface.hh make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./phase.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./phase.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./line_average.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./line_average.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./surface_builder.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./surface_builder.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./physical_units.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./physical_units.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_node_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src/./rscrosscorr.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/./rscrosscorr.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/tiff_util.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/tiff_util.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./builder.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./builder.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_node_visitor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./pixel_sampling.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./pixel_sampling.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_text_document_layout.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/python_shell_text_document_layout.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/geom/pymod/CMakeFiles/_ost_geom.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/img/jpk_util.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/jpk_util.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./point_list.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./point_list.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./surface_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./surface_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_object_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_object_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/shell_history.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/shell_history.hh [ 3%] Built target _ost_geom [ 3%] Built target ost_img_alg_headers make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/info/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/src/CMakeFiles/ost_info.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/state_machine.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/state_machine.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_object.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_object.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./surface_prop.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./surface_prop.hh [ 3%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_composite2.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./point.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./point.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/state.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/state.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_object_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_object_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/fasta_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./torsion_handle.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./torsion_handle.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./polygon_mask.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./polygon_mask.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/transition.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/transition.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_prim.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_prim.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./transfer_connectivity.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./transfer_connectivity.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./progress.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./progress.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/python_shell/transition_guard.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./symmetry_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./symmetry_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./size.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./size.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./query_view_wrapper.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./query_view_wrapper.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/button_bar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/button_bar.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gfx_test_object.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gfx_test_object.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/profile_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./spherical_mask.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./spherical_mask.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/drop_box.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/drop_box.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./glwin_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./glwin_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./view_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/hhm_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/hhm_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./util.cc /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./util.cc make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/panel_bar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/panel_bar.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./input.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./input.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./view_type_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./view_type_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/pssm_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/pssm_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./util.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./util.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/panel_manager.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/panel_manager.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./prim_list.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./prim_list.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/info/src/CMakeFiles/ost_info.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./view_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/bottom_bar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/bottom_bar.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./value_util.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./value_util.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./scene.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./scene.hh [ 4%] Built target ost_info cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./xcs_editor.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./xcs_editor.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/load.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/load.hh make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/pymod/CMakeFiles/_ost_base.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./vecmat.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./vecmat.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/button_box.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/button_box.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./selection.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./selection.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/seq/save.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/save.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./bounding_box.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./bounding_box.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/img/base/src/./mask_info_convert.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/./mask_info_convert.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/event_button.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/event_button.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./binary_data_sink.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./binary_data_sink.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./transform.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./transform.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./surface.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./surface.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/panel_widget_container.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/panel_widget_container.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./io_manager.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./io_manager.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./texture.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./texture.hh [ 4%] Built target ost_img_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/panel_bar_widget_holder.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/panel_bar_widget_holder.hh make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/depend cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./binary_data_source.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./binary_data_source.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/src/CMakeFiles/ost_img.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./vertex_array.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./vertex_array.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/side_bar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/side_bar.hh make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/build [ 4%] Built target ost_mol_headers make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/mol/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./vertex_array_helper.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./container_serialization.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./container_serialization.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/splitter_panel_bar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/splitter_panel_bar.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/base/pymod/CMakeFiles/_ost_base.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./scene_observer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./scene_observer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./swap_util.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./swap_util.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/panels/tabbed_panel_bar.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/panels/tabbed_panel_bar.hh [ 4%] Built target _ost_base cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./io_utils.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./io_utils.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gl_include.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gl_include.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/context_menu.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./io_exception.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./io_exception.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./glext_include.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./glext_include.hh [ 5%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/current_selection_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_mat2.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./render_mode.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./render_mode.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./convert.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./convert.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/custom_part_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./material.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./material.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./converting_streams.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./converting_streams.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/entity_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/entity_part_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gradient.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gradient.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./formatted_line.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./formatted_line.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gradient_manager.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gradient_manager.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/gfx_scene_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/chemdict_parser.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./chemdict_parser.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/star_parser.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./star_parser.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/label_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/label_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/root_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/root_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/mmcif_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./mmcif_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./primitives.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./primitives.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/render_mode_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/mmcif_info.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./mmcif_info.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./povray_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./povray_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/render_modes_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/io_profile.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./io_profile.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./povray.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./povray.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_node.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./exporter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./exporter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/dcd_io.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./dcd_io.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/entity_io_crd_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./entity_io_crd_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./exporter_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./exporter_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./gost_exporter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./gost_exporter.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/entity_io_pqr_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/messages/message_widget.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/messages/message_widget.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./color_ops/map_handle_color_op.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./map_handle_color_op.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/entity_io_mae_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/messages/message_box_widget.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/entity_io_mmcif_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/messages/log_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/messages/log_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./map_iso.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./map_iso.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/argand.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/argand.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/entity_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./entity_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./map_slab.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./map_slab.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/pdb_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./pdb_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gfx/src/./map_iso_prop.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/./map_iso_prop.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/entity_io_pdb_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./entity_io_pdb_handler.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/img/base/src/CMakeFiles/ost_img.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 5%] Built target ost_gfx_headers cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/pdb_writer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./pdb_writer.hh make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/info/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/info/pymod/CMakeFiles/_ost_info.dir/DependInfo.cmake --color= [ 8%] Built target ost_img make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/depend cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/entity_io_sdf_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/draw_overlay.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/sdf_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./sdf_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/drawing_functions.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/sdf_writer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./sdf_writer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/fft_panel.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/info/pymod/CMakeFiles/_ost_info.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/info_panel.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/save_entity.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./save_entity.hh [ 9%] Built target _ost_info make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/pymod/CMakeFiles/_ost_img.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/img2qt.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/load_entity.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./load_entity.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/mask_overlay.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/surface_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./surface_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/null_overlay.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/null_overlay.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/load_surface.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./load_surface.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/overlay.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/surface_io_msms_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/pdb_str.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./pdb_str.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/stereochemical_params_reader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./mol/omf.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./omf.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/sequence_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_gui.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_gui.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_observer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_observer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/fasta_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/mol/base/src/CMakeFiles/ost_mol.dir/build.make modules/mol/base/src/CMakeFiles/ost_mol.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/pir_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./pir_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay_base.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay_base.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/promod_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./promod_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/strategies.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/profile_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./profile_io_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/strategies_fw.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/strategies_fw.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/hhm_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./hhm_io_handler.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/base/pymod/CMakeFiles/_ost_img.dir/build.make modules/img/base/pymod/CMakeFiles/_ost_img.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/data_viewer/viewer_normalizer.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/pssm_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./pssm_io_handler.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/mol/base/src/CMakeFiles/ost_mol.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./file_browser.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./file_browser.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/clustal_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./clustal_io_handler.hh [ 14%] Built target ost_mol cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./file_type_dialog.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./file_type_dialog.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/img/base/pymod/CMakeFiles/_ost_img.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/load.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./load.hh [ 14%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_mat3.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./file_viewer.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./file_viewer.hh [ 17%] Built target _ost_img make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build.make modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./seq/save.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./save.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./gl_canvas.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./gl_canvas.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/load_map.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./load_map.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./gl_win.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./gl_win.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_df3_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_df3_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./scene_menu.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./scene_menu.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/image_format.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./image_format.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./gosty_app.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./gosty_app.hh [ 21%] Built target ost_img_alg make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/depend cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_dx_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_dx_handler.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/mol/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./admin.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./admin.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_spi_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_spi_handler.hh make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./module_config.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./module_config.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_situs_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_situs_handler.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/seq/base/src/CMakeFiles/ost_seq.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./main.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./main.hh [ 22%] Built target ost_seq cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_handler.hh make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/alg/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./main_area.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./main_area.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_mrc_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_mrc_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./perspective.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./perspective.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_dat_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_dat_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./scene_selection.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./scene_selection.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_ipl_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_ipl_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./main_window.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./main_window.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_jpk_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_jpk_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./dock_widget.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./dock_widget.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build.make modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./dock_widget.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./dock_widget.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_nanoscope_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_nanoscope_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_png_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_png_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./thin_splitter.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./thin_splitter.hh make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_dm3_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_dm3_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./widget.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./widget.hh [ 22%] Built target _ost_img_alg make -f modules/base/tests/CMakeFiles/ost_base_tests.dir/build.make modules/base/tests/CMakeFiles/ost_base_tests.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/tests/CMakeFiles/ost_base_tests.dir/DependInfo.cmake --color= cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./widget_geom_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./widget_geom_handler.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/map_io_tiff_handler.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./map_io_tiff_handler.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/base/tests/CMakeFiles/ost_base_tests.dir/build.make modules/base/tests/CMakeFiles/ost_base_tests.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./widget_pool.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./widget_pool.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/tiff_util.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./tiff_util.hh [ 22%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o -MF CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o.d -o CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/tests/test_generic_property.cc cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/io/src/./img/jpk_util.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/./jpk_util.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./widget_registry.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./widget_registry.hh cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./widget_state_saver.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./widget_state_saver.hh make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/modules/gui/src/./file_loader.hh /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gui/./file_loader.hh [ 22%] Built target ost_io_headers make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/bindings/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 22%] Built target ost_gui_headers make -f modules/img/base/tests/CMakeFiles/ost_img_tests.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/tests/CMakeFiles/ost_img_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/bindings/src/CMakeFiles/ost_bindings.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/base/tests/CMakeFiles/ost_img_tests.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build [ 22%] Built target ost_bindings [ 22%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_data.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_data.cc.o -MF CMakeFiles/ost_img_tests.dir/test_data.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_data.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_data.cc make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 22%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_clear.cc make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 24%] Built target _ost_mol make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 24%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_atom_groups.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_composite3.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_composite3.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_composite2.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_mat2.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_mat3.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_clear.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_clear.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_data.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_data.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_data.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/base/tests/test_generic_property.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/base/tests/test_generic_property.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_atom_groups.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_atom_groups.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 24%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_extent.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_extent.cc.o -MF CMakeFiles/ost_img_tests.dir/test_extent.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_extent.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_extent.cc [ 24%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_conj.cc [ 24%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_mat4.cc [ 24%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op2.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_op2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_op2.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_op2.cc [ 24%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op3.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_op3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_op3.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_op3.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_extent.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_extent.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_conj.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_conj.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_mat4.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_op2.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 24%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_chain.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_chain.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_chain.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_chain.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc [ 24%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op4.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op4.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_op4.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_op4.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_op4.cc [ 24%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_convolute.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_op3.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o -MF CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o.d -o CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/tests/test_string_ref.cc [ 25%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image.cc.o -MF CMakeFiles/ost_img_tests.dir/test_image.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_image.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_image.cc [ 25%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_quat.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_quat.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_quat.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_quat.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_quat.cc [ 25%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_vec2.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_convolute.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_convolute.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_op4.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_quat.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_vec3.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_vec2.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_discrete_shrink.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_image.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_image.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_vec4.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_vec3.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 25%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o -MF CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o.d -o CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/tests/test_pod_vector.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_discrete_shrink.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_discrete_shrink.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 26%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_transform.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_transform.cc.o -MF CMakeFiles/ost_geom_tests.dir/test_transform.cc.o.d -o CMakeFiles/ost_geom_tests.dir/test_transform.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_transform.cc [ 26%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/tests.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -MD -MT modules/geom/tests/CMakeFiles/ost_geom_tests.dir/tests.cc.o -MF CMakeFiles/ost_geom_tests.dir/tests.cc.o.d -o CMakeFiles/ost_geom_tests.dir/tests.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/tests.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_vec4.cc:20: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/stdexcept:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_fft.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_transform.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/geom/tests/test_transform.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_fill.cc [ 27%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/tests.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/base/tests/CMakeFiles/ost_base_tests.dir/tests.cc.o -MF CMakeFiles/ost_base_tests.dir/tests.cc.o.d -o CMakeFiles/ost_base_tests.dir/tests.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/base/tests/tests.cc [ 27%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_filter.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_fft.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_fft.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_histogram.cc [ 27%] Linking CXX executable ../../../tests/ost_base_tests cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_base_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o CMakeFiles/ost_base_tests.dir/test_pod_vector.cc.o CMakeFiles/ost_base_tests.dir/tests.cc.o -o ../../../tests/ost_base_tests -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib /usr/lib/i386-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 [ 27%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state.cc.o -MF CMakeFiles/ost_img_tests.dir/test_image_state.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_image_state.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_image_state.cc make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 27%] Built target ost_base_tests [ 27%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o -MF CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_fill.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_fill.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_filter.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_filter.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Linking CXX executable ../../../tests/ost_geom_tests cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_geom_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o CMakeFiles/ost_geom_tests.dir/test_mat4.cc.o CMakeFiles/ost_geom_tests.dir/test_op2.cc.o CMakeFiles/ost_geom_tests.dir/test_op3.cc.o CMakeFiles/ost_geom_tests.dir/test_op4.cc.o CMakeFiles/ost_geom_tests.dir/test_quat.cc.o CMakeFiles/ost_geom_tests.dir/test_vec2.cc.o CMakeFiles/ost_geom_tests.dir/test_vec3.cc.o CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o CMakeFiles/ost_geom_tests.dir/test_transform.cc.o CMakeFiles/ost_geom_tests.dir/tests.cc.o -o ../../../tests/ost_geom_tests -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib /usr/lib/i386-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 27%] Built target ost_geom_tests make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 27%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_sequence.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/alg/histogram.hh:30, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_histogram.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_histogram.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:53: In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void mol_base::throw_invalid_chain_handle::test_method()' at /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:114:18: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ In file included from /usr/include/boost/variant.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In member function 'void mol_base::throw_invalid_chain_handle::test_method()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void mol_base::throw_invalid_chain_handle::test_method()' at /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:114:18: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void mol_base::throw_invalid_chain_handle::test_method()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void mol_base::throw_invalid_chain_handle::test_method()' at /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:114:18: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[1]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void mol_base::throw_invalid_chain_handle::test_method()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In member function 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::size_type std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::length() const [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]', inlined from 'std::__cxx11::basic_string<_CharT, _Traits, _Alloc>& std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::operator=(std::__cxx11::basic_string<_CharT, _Traits, _Alloc>&&) [with _CharT = char; _Traits = std::char_traits; _Alloc = std::allocator]' at /usr/include/c++/12/bits/basic_string.h:891:15, inlined from 'void boost::detail::variant::move_storage::internal_visit(T&, int) const [with T = std::__cxx11::basic_string]' at /usr/include/boost/variant/variant.hpp:597:21, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke_impl(int, Visitor&, VoidPtrCV, T*, mpl_::true_) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string]' at /usr/include/boost/variant/detail/visitation_impl.hpp:117:34, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl_invoke(int, Visitor&, VoidPtrCV, T*, NoBackupFlag, int) [with Visitor = move_storage; VoidPtrCV = void*; T = std::__cxx11::basic_string; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:157:41, inlined from 'typename Visitor::result_type boost::detail::variant::visitation_impl(int, int, Visitor&, VoidPtrCV, mpl_::false_, NoBackupFlag, Which*, step0*) [with Which = mpl_::int_<0>; step0 = visitation_impl_step, std::__cxx11::basic_string, boost::mpl::l_item, float, boost::mpl::l_item, int, boost::mpl::l_item, bool, boost::mpl::l_item, geom::Vec3, boost::mpl::l_end> > > > > >, boost::mpl::l_iter >; Visitor = move_storage; VoidPtrCV = void*; NoBackupFlag = boost::variant, float, int, bool, geom::Vec3>::has_fallback_type_]' at /usr/include/boost/variant/detail/visitation_impl.hpp:238:5, inlined from 'static typename Visitor::result_type boost::variant::internal_apply_visitor_impl(int, int, Visitor&, VoidPtrCV) [with Visitor = boost::detail::variant::move_storage; VoidPtrCV = void*; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2337:48, inlined from 'typename Visitor::result_type boost::variant::internal_apply_visitor(Visitor&) [with Visitor = boost::detail::variant::move_storage; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2349:43, inlined from 'void boost::variant::variant_assign(boost::variant&&) [with T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2081:41, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2108:27, inlined from 'void boost::variant::assign(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2095:10, inlined from 'typename boost::enable_if >, boost::detail::variant::is_variant_constructible_from::is_recursive_, boost::mpl::transform::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type, boost::mpl::protect > > >, boost::mpl::identity::is_sequence_based_, typename boost::mpl::eval_if::is_recursive_, T0_, boost::mpl::identity >::type, boost::detail::variant::make_variant_list::is_recursive_, T0_, boost::mpl::identity >::type, TN ...> >::type> >::type, boost::mpl::protect > >::type> >, boost::variant&>::type boost::variant::operator=(const T&) [with T = int; T0_ = std::__cxx11::basic_string; TN = {float, int, bool, geom::Vec3}]' at /usr/include/boost/variant/variant.hpp:2159:15, inlined from 'void ost::GenericPropContainer::SetIntProp(const String&, int) [with H = ost::mol::ResidueBase]' at /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void mol_base::throw_invalid_chain_handle::test_method()' at /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:114:18: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '((const __vector(1) unsigned int*)((char*)&temp + offsetof(boost::variant, std::allocator >, float, int, bool, geom::Vec3>,boost::variant, std::allocator >, float, int, bool, geom::Vec3>::storage_.boost::aligned_storage<24, 4>::.boost::detail::aligned_storage::aligned_storage_imp<24, 4>::data_)))[2]' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void mol_base::throw_invalid_chain_handle::test_method()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 27%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_image_state.cc:32: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_image_state.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_conn.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_conn.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_conn.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_conn.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_conn.cc [ 27%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_mirror.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_sequence.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_sequence.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 27%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_negate.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_conn.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_mirror.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_mirror.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 28%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_point.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_point.cc.o -MF CMakeFiles/ost_img_tests.dir/test_point.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_point.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_point.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_negate.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_negate.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 28%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_coord_group.cc [ 28%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_sampling.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_sampling.cc.o -MF CMakeFiles/ost_img_tests.dir/test_sampling.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_sampling.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_sampling.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_point.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_point.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_point.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 28%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_power_spectrum.cc [ 28%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_shift.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_coord_group.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_coord_group.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 28%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc [ 28%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_domains.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_domains.cc.o -MF CMakeFiles/ost_img_tests.dir/test_domains.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_domains.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_domains.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_sampling.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_sampling.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_sampling.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_power_spectrum.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_power_spectrum.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_shift.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_shift.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 28%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_size.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_size.cc.o -MF CMakeFiles/ost_img_tests.dir/test_size.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_size.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_size.cc [ 28%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_builder.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_builder.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_builder.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_builder.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_builder.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 28%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_stat.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/istream:38, from /usr/include/c++/12/sstream:38, from /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_domains.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/builder.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_builder.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/builder.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 28%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_transform.cc [ 29%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_normalizer.cc [ 29%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o -MF CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/test_value_holder.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:29:43: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 29 | class AlignedColumnIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_stat.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/tests.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/base/tests/CMakeFiles/ost_img_tests.dir/tests.cc.o -MF CMakeFiles/ost_img_tests.dir/tests.cc.o.d -o CMakeFiles/ost_img_tests.dir/tests.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests/tests.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_transform.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_transform.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_normalizer.cc:35: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /usr/include/c++/12/iostream:39, from /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/test_normalizer.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 29%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_profile.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_profile.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_profile.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_profile.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/test_profile.cc [ 29%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_delete.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_delete.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_delete.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_delete.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_delete.cc [ 29%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_entity.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_entity.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_entity.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_entity.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_entity.cc [ 29%] Linking CXX executable ../../../../tests/ost_img_tests cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_img_tests.dir/test_data.cc.o CMakeFiles/ost_img_tests.dir/test_extent.cc.o CMakeFiles/ost_img_tests.dir/test_image.cc.o CMakeFiles/ost_img_tests.dir/test_image_state.cc.o CMakeFiles/ost_img_tests.dir/test_image_state_visitor.cc.o CMakeFiles/ost_img_tests.dir/test_index.cc.o CMakeFiles/ost_img_tests.dir/test_point.cc.o CMakeFiles/ost_img_tests.dir/test_sampling.cc.o CMakeFiles/ost_img_tests.dir/test_domains.cc.o CMakeFiles/ost_img_tests.dir/test_size.cc.o CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o CMakeFiles/ost_img_tests.dir/tests.cc.o -o ../../../../tests/ost_img_tests -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib /usr/lib/i386-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 29%] Built target ost_img_tests [ 29%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_ics.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_ics.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_ics.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_ics.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_ics.cc [ 29%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/tests.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/tests.cc.o -MF CMakeFiles/ost_img_alg_tests.dir/tests.cc.o.d -o CMakeFiles/ost_img_alg_tests.dir/tests.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests/tests.cc [ 29%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_query.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_query.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_query.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_query.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_query.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_delete.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_delete.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_surface.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_surface.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_surface.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_surface.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_surface.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec_mat_predicates.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_entity.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_entity.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 30%] Linking CXX executable ../../../../tests/ost_img_alg_tests cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img_alg_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o CMakeFiles/ost_img_alg_tests.dir/test_discrete_shrink.cc.o CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o CMakeFiles/ost_img_alg_tests.dir/test_histogram.cc.o CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o CMakeFiles/ost_img_alg_tests.dir/tests.cc.o -o ../../../../tests/ost_img_alg_tests -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib /usr/lib/i386-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_ics.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_ics.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 30%] Built target ost_img_alg_tests make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 32%] Built target ost_seq_alg make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build.make modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 32%] Built target _ost_seq make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/db/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/src/CMakeFiles/ost_db.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/db/src/CMakeFiles/ost_db.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 34%] Built target ost_db make -f modules/base/tests/CMakeFiles/ost_base_tests_run.dir/build.make modules/base/tests/CMakeFiles/ost_base_tests_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/tests/CMakeFiles/ost_base_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/base/tests/CMakeFiles/ost_base_tests_run.dir/build.make modules/base/tests/CMakeFiles/ost_base_tests_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 34%] running checks for module base cd /build/reproducible-path/openstructure-2.3.1/modules/base/tests && env OST_ROOT=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/tests/ost_base_tests Running 5 test cases... *** No errors detected make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 34%] Built target ost_base_tests_run make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/bindings/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/DependInfo.cmake --color= In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build.make modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 34%] Built target _ost_bindings make -f modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/geom/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/build.make modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 34%] running checks for module geom cd /build/reproducible-path/openstructure-2.3.1/modules/geom/tests && env OST_ROOT=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/tests/ost_geom_tests Running 25 test cases... *** No errors detected make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 34%] Built target ost_geom_tests_run make -f modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/build.make modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 34%] running checks for module img cd /build/reproducible-path/openstructure-2.3.1/modules/img/base/tests && env OST_ROOT=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/tests/ost_img_tests Running 44 test cases... *** No errors detected [ 34%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/tests.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/tests.cc.o -MF CMakeFiles/ost_seq_tests.dir/tests.cc.o.d -o CMakeFiles/ost_seq_tests.dir/tests.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests/tests.cc make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 34%] Built target ost_img_tests_run make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/build.make modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 34%] running checks for module img_alg cd /build/reproducible-path/openstructure-2.3.1/modules/img/alg/tests && env OST_ROOT=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/tests/ost_img_alg_tests [ 34%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_residue.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_residue.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_residue.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_residue.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_residue.cc Running 25 test cases... *** No errors detected make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 34%] Built target ost_img_alg_tests_run make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 34%] Built target _ost_seq_alg make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/conop/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/src/CMakeFiles/ost_conop.dir/DependInfo.cmake --color= In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_surface.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_surface.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/conop/src/CMakeFiles/ost_conop.dir/build.make modules/conop/src/CMakeFiles/ost_conop.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/conop/src/CMakeFiles/ost_conop.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 35%] Built target ost_conop make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/db/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/db/pymod/CMakeFiles/_ost_db.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/db/pymod/CMakeFiles/_ost_db.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 36%] Built target _ost_db make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build.make modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 38%] Built target ost_mol_alg make -f modules/conop/tests/CMakeFiles/ost_conop_tests.dir/build.make modules/conop/tests/CMakeFiles/ost_conop_tests.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/conop/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/tests/CMakeFiles/ost_conop_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/conop/tests/CMakeFiles/ost_conop_tests.dir/build.make modules/conop/tests/CMakeFiles/ost_conop_tests.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 39%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o -MF CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o.d -o CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/tests/test_amino_acids.cc [ 39%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o -MF CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o.d -o CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/tests/test_heuristic_conop.cc [ 40%] Linking CXX executable ../../../../tests/ost_seq_tests cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o CMakeFiles/ost_seq_tests.dir/test_profile.cc.o CMakeFiles/ost_seq_tests.dir/tests.cc.o -o ../../../../tests/ost_seq_tests -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib /usr/lib/i386-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 40%] Built target ost_seq_tests make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gfx/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx.dir/DependInfo.cmake --color= [ 40%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_view.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_view.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_view.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_residue.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_residue.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/conop/tests/test_heuristic_conop.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/c++/12/bits/locale_classes.h:40, from /usr/include/c++/12/bits/ios_base.h:41, from /usr/include/c++/12/ios:42, from /usr/include/c++/12/ostream:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/log.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/conop/tests/test_heuristic_conop.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/gfx/src/CMakeFiles/ost_gfx.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 46%] Built target ost_gfx make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/conop/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/pymod/CMakeFiles/_ost_conop.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/conop/pymod/CMakeFiles/_ost_conop.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 47%] Built target _ost_conop make -f modules/io/src/CMakeFiles/ost_io.dir/build.make modules/io/src/CMakeFiles/ost_io.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/io/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/src/CMakeFiles/ost_io.dir/DependInfo.cmake --color= In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/amino_acids.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/conop/tests/test_amino_acids.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/conop/tests/test_amino_acids.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/conop/amino_acids.hh:61:42: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 61 | class AminoAcidSetIterator : public std::iterator struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_view.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 55%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o -MF CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/tests/test_gfx_node.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/builder.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_transfer_connectivity.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/builder.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 55%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/tests.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/tests.cc.o -MF CMakeFiles/ost_conop_tests.dir/tests.cc.o.d -o CMakeFiles/ost_conop_tests.dir/tests.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/tests/tests.cc [ 55%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_view_op.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/tests/test_gfx_node.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/gfx_node.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/tests/test_gfx_node.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 55%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/tests.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/tests.cc.o -MF CMakeFiles/ost_mol_tests.dir/tests.cc.o.d -o CMakeFiles/ost_mol_tests.dir/tests.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/tests.cc [ 55%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o -MF CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o.d -o CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/tests/test_rule_based_conop.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_view_op.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/mol/base/tests/test_view_op.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 55%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/helper.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/conop/tests/CMakeFiles/ost_conop_tests.dir/helper.cc.o -MF CMakeFiles/ost_conop_tests.dir/helper.cc.o.d -o CMakeFiles/ost_conop_tests.dir/helper.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/conop/tests/helper.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/conop/tests/test_rule_based_conop.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/conop/tests/test_rule_based_conop.cc:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 56%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_color.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_color.cc.o -MF CMakeFiles/ost_gfx_tests.dir/test_color.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/test_color.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/tests/test_color.cc [ 56%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o -MF CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/gfx/tests/test_map_octree.cc make -f modules/io/tests/CMakeFiles/ost_io_tests.dir/build.make modules/io/tests/CMakeFiles/ost_io_tests.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/io/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests/CMakeFiles/ost_io_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/io/tests/CMakeFiles/ost_io_tests.dir/build.make modules/io/tests/CMakeFiles/ost_io_tests.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 56%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_clustal.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_clustal.cc.o -MF CMakeFiles/ost_io_tests.dir/test_clustal.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_clustal.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_clustal.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/conop/tests/helper.cc:3: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/conop/tests/helper.cc:2: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make -f modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/build.make modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/build.make modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 56%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/tests/test_superposition.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/tests/test_color.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/iterator:61, from /usr/include/boost/operators.hpp:98, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/color.hh:28: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/data.hh:36, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/gfx/tests/test_map_octree.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/memory:63, from /usr/include/boost/smart_ptr/detail/sp_counted_impl.hpp:35, from /usr/include/boost/smart_ptr/detail/shared_count.hpp:27, from /usr/include/boost/smart_ptr/shared_ptr.hpp:17, from /usr/include/boost/shared_ptr.hpp:17, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image_handle.hh:32: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_clustal.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_clustal.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/build.make modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 56%] running checks for module seq cd /build/reproducible-path/openstructure-2.3.1/modules/seq/base/tests && env OST_ROOT=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/tests/ost_seq_tests Running 32 test cases... *** No errors detected make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 56%] Built target ost_seq_tests_run make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/build.make modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 56%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/tests/test_superposition.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/bits/specfun.h:45, from /usr/include/c++/12/cmath:1935, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/base.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:26: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 56%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/tests/test_merge_pairwise_alignments.cc [ 56%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc:28: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/clip_alignment.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc:30: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 56%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_crd.cc [ 56%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/tests/tests.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/merge_pairwise_alignments.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/tests/test_merge_pairwise_alignments.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/tests/test_merge_pairwise_alignments.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 56%] Linking CXX executable ../../../tests/ost_gfx_tests cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_gfx_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_gfx_tests.dir/tests.cc.o CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o CMakeFiles/ost_gfx_tests.dir/test_color.cc.o CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o -o ../../../tests/ost_gfx_tests -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib /usr/lib/i386-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_gfx.so.2.3.1 ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/i386-linux-gnu/libOpenGL.so /usr/lib/i386-linux-gnu/libGLX.so /usr/lib/i386-linux-gnu/libGLU.so ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/i386-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so /usr/lib/i386-linux-gnu/libboost_program_options.so /usr/lib/i386-linux-gnu/libboost_thread.so /usr/lib/i386-linux-gnu/libboost_chrono.so /usr/lib/i386-linux-gnu/libboost_date_time.so /usr/lib/i386-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libtiff.so /usr/lib/i386-linux-gnu/libpng.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 56%] Built target ost_gfx_tests make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gfx/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 58%] Built target _ost_gfx make -f modules/gui/src/CMakeFiles/ost_gui.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gui/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/src/CMakeFiles/ost_gui.dir/DependInfo.cmake --color= In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/vec_mat_predicates.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 58%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/tests/test_consistency_checks.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc:33: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_crd.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_crd.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gui/src/CMakeFiles/ost_gui.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/gui/src/CMakeFiles/ost_gui.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 91%] Built target ost_gui make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/io/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/pymod/CMakeFiles/_ost_io.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/io/pymod/CMakeFiles/_ost_io.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 91%] Built target _ost_io make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gfx/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 91%] running checks for module gfx cd /build/reproducible-path/openstructure-2.3.1/modules/gfx/tests && env OST_ROOT=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/tests/ost_gfx_tests Running 13 test cases... *** No errors detected make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 91%] Built target ost_gfx_tests_run make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/gui/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/gui/pymod/CMakeFiles/_ost_gui.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Nothing to be done for 'modules/gui/pymod/CMakeFiles/_ost_gui.dir/build'. make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 93%] Built target _ost_gui make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts/CMakeFiles/ost_scripts.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_config /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/openstructure/libexec/ost_config cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/bin/ost In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/tests/test_consistency_checks.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/tests/test_consistency_checks.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different dng /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/bin/dng cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_startup.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/ost_startup.py cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/reproducible-path/openstructure-2.3.1/scripts/dng_startup.py /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages//ost/dng_startup.py make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 93%] Built target ost_scripts make -f modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/build.make modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 93%] running checks test_aaindex.py cd /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/tests/test_aaindex.py" . ---------------------------------------------------------------------- Ran 1 test in 0.109s OK make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 93%] Built target test_aaindex.py_run make -f modules/base/tests/CMakeFiles/test_stutil.py_run.dir/build.make modules/base/tests/CMakeFiles/test_stutil.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/tests/CMakeFiles/test_stutil.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/base/tests/CMakeFiles/test_stutil.py_run.dir/build.make modules/base/tests/CMakeFiles/test_stutil.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 93%] running checks test_stutil.py cd /build/reproducible-path/openstructure-2.3.1/modules/base/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.3.1/modules/base/tests/test_stutil.py" ...... ---------------------------------------------------------------------- Ran 6 tests in 0.001s OK make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 93%] Built target test_stutil.py_run make -f modules/base/tests/CMakeFiles/test_table.py_run.dir/build.make modules/base/tests/CMakeFiles/test_table.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/tests/CMakeFiles/test_table.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/base/tests/CMakeFiles/test_table.py_run.dir/build.make modules/base/tests/CMakeFiles/test_table.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 93%] running checks test_table.py cd /build/reproducible-path/openstructure-2.3.1/modules/base/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.3.1/modules/base/tests/test_table.py" [ 93%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/tests/test_sequence_identity.cc [ 93%] Linking CXX executable ../../../../tests/ost_mol_tests cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/base/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o CMakeFiles/ost_mol_tests.dir/test_chain.cc.o CMakeFiles/ost_mol_tests.dir/test_conn.cc.o CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o CMakeFiles/ost_mol_tests.dir/test_builder.cc.o CMakeFiles/ost_mol_tests.dir/test_delete.cc.o CMakeFiles/ost_mol_tests.dir/test_entity.cc.o CMakeFiles/ost_mol_tests.dir/test_ics.cc.o CMakeFiles/ost_mol_tests.dir/test_query.cc.o CMakeFiles/ost_mol_tests.dir/test_surface.cc.o CMakeFiles/ost_mol_tests.dir/test_residue.cc.o CMakeFiles/ost_mol_tests.dir/test_view.cc.o CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o CMakeFiles/ost_mol_tests.dir/tests.cc.o -o ../../../../tests/ost_mol_tests -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib /usr/lib/i386-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 [ 93%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o -MF CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o.d -o CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc [ 94%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o -MF CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o.d -o CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/tests/tests.cc make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 94%] Built target ost_mol_tests make -f modules/base/tests/CMakeFiles/test_log.py_run.dir/build.make modules/base/tests/CMakeFiles/test_log.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/base/tests/CMakeFiles/test_log.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/base/tests/CMakeFiles/test_log.py_run.dir/build.make modules/base/tests/CMakeFiles/test_log.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 94%] running checks test_log.py cd /build/reproducible-path/openstructure-2.3.1/modules/base/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.3.1/modules/base/tests/test_log.py" .... ---------------------------------------------------------------------- Ran 4 tests in 0.017s OK make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 94%] Built target test_log.py_run make -f modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 94%] running checks test_msms.py cd /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests/test_msms.py" [ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_dcd.cc .......................Could not find msms executable: ignoring unit tests make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 95%] Built target test_msms.py_run make -f modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/DependInfo.cmake --color= make -f modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/depend make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/DependInfo.cmake --color= [ 95%] running checks test_clustalw.py cd /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests/test_clustalw.py" make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 95%] running checks test_hhblits.py cd /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests/test_hhblits.py" No HHblits installation found: skip unit tests make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 95%] Built target test_hhblits.py_run make -f modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' .[ 95%] running checks test_blast.py cd /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests/test_blast.py" In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alg/sequence_identity.hh:26, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/tests/test_sequence_identity.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/seq/alg/tests/test_sequence_identity.cc:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ Could not find blast executable: ignoring unit tests make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 95%] Built target test_blast.py_run make -f modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 95%] running checks test_kclust.py cd /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests/test_kclust.py" Could not find kClust executable: ignoring unit tests make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 95%] Built target test_kclust.py_run make -f modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 95%] running checks test_naccess.py cd /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests/test_naccess.py" In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc:21: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:22: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ FCould not find NACCESS, could not test binding... .make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 95%] Built target test_naccess.py_run make -f modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/depend make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/reproducible-path/openstructure-2.3.1 /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/tests /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/build make[4]: Entering directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' .[ 95%] running checks test_cadscore.py cd /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/reproducible-path/openstructure-2.3.1/modules/bindings/tests/test_cadscore.py" ... ====================================================================== FAIL: testMultipleClustalW (__main__.TestClustalWBindings.testMultipleClustalW) ---------------------------------------------------------------------- Traceback (most recent call last): File "/build/reproducible-path/openstructure-2.3.1/modules/bindings/tests/test_clustalw.py", line 45, in testMultipleClustalW assert self.mult_alignment.ToString(80) == aln.ToString(80), \ ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AssertionError: Multiple alignment differs from precomputed one ---------------------------------------------------------------------- Ran 7 tests in 1.495s FAILED (failures=1) make[4]: *** [modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/build.make:74: modules/bindings/tests/CMakeFiles/test_clustalw.py_run] Error 1 make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:2186: modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/all] Error 2 make[3]: *** Waiting for unfinished jobs.... [ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_sdf.cc ................In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/lib/python3.11/unittest/case.py:579: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/enrichment-out.png'> if method() is not None: ResourceWarning: Enable tracemalloc to get the object allocation traceback ..In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/coord_group.hh:29, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/dcd_io.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_dcd.cc:23: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_dcd.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/lib/python3.11/unittest/case.py:579: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/roc-out.png'> if method() is not None: ResourceWarning: Enable tracemalloc to get the object allocation traceback ./usr/lib/python3.11/unittest/case.py:579: ResourceWarning: unclosed file <_io.BufferedReader name='testfiles/roc-same-val-out.png'> if method() is not None: ResourceWarning: Enable tracemalloc to get the object allocation traceback ................./build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib/python3.11/dist-packages/ost/table.py:2186: DeprecationWarning: scipy.isnan is deprecated and will be removed in SciPy 2.0.0, use numpy.isnan instead if scipy.isnan(correl): ......................... ---------------------------------------------------------------------- Ran 83 tests in 3.933s OK make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 95%] Built target test_table.py_run [ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_sequence_profile.cc [ 95%] Linking CXX executable ../../../../tests/ost_seq_alg_tests cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/seq/alg/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_seq_alg_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o -o ../../../../tests/ost_seq_alg_tests -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib /usr/lib/i386-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/i386-linux-gnu/libsqlite3.so /usr/lib/i386-linux-gnu/libboost_program_options.so /usr/lib/i386-linux-gnu/libboost_thread.so /usr/lib/i386-linux-gnu/libboost_chrono.so /usr/lib/i386-linux-gnu/libboost_date_time.so /usr/lib/i386-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libtiff.so /usr/lib/i386-linux-gnu/libpng.so /usr/lib/i386-linux-gnu/libz.so In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_sdf.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_sdf.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/load.hh:27, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_sequence_profile.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_sequence_profile.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 95%] Built target ost_seq_alg_tests [ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_pir.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_pir.cc.o -MF CMakeFiles/ost_io_tests.dir/test_pir.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_pir.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_pir.cc [ 95%] Linking CXX executable ../../../../tests/ost_mol_alg_tests cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/mol/alg/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_alg_tests.dir/link.txt --verbose=1 In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o -o ../../../../tests/ost_mol_alg_tests -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib /usr/lib/i386-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_program_options.so /usr/lib/i386-linux-gnu/libboost_thread.so /usr/lib/i386-linux-gnu/libboost_chrono.so /usr/lib/i386-linux-gnu/libboost_date_time.so /usr/lib/i386-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 ../../../../stage/lib/libost_seq.so.2.3.1 ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libsqlite3.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libtiff.so /usr/lib/i386-linux-gnu/libpng.so /usr/lib/i386-linux-gnu/libz.so [ 95%] Linking CXX executable ../../../tests/ost_conop_tests cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/conop/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_conop_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o CMakeFiles/ost_conop_tests.dir/tests.cc.o CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o CMakeFiles/ost_conop_tests.dir/helper.cc.o -o ../../../tests/ost_conop_tests -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib /usr/lib/i386-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/i386-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 95%] Built target ost_conop_tests make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o -MF CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_iomanager.cc [ 95%] Built target ost_mol_alg_tests [ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/tests.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/tests.cc.o -MF CMakeFiles/ost_io_tests.dir/tests.cc.o.d -o CMakeFiles/ost_io_tests.dir/tests.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/tests/tests.cc [ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o -MF CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_star_parser.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_pir.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_pir.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o -MF CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_mmcif_reader.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_iomanager.cc:22: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_iomanager.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_star_parser.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_star_parser.cc:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o -MF CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_mmcif_info.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_mmcif_reader.cc:26: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_mmcif_reader.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_img.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_img.cc.o -MF CMakeFiles/ost_io_tests.dir/test_io_img.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_io_img.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_img.cc [ 96%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/i386-linux-gnu/qt5 -isystem /usr/include/i386-linux-gnu/qt5/QtXml -isystem /usr/include/i386-linux-gnu/qt5/QtCore -isystem /usr/lib/i386-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/i386-linux-gnu/qt5/QtGui -isystem /usr/include/i386-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -fPIC -MD -MT modules/io/tests/CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o -MF CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o.d -o CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o -c /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_exceptions.cc In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh:25, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_mmcif_info.cc:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh:32:17: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 32 | : public std::iterator{ | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_mmcif_info.cc:21: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/map.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/load_map.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_exceptions.cc:27: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_exceptions.cc:25: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/point.hh:35, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/image.hh:34, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/img/map.hh:22, from /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/io/img/load_map.hh:24, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_img.cc:29: /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class const_circular_iter : public std::iterator | ^~~~~~~~ In file included from /usr/include/c++/12/string:45, from /usr/include/boost/test/utils/basic_cstring/bcs_char_traits.hpp:25, from /usr/include/boost/test/utils/basic_cstring/basic_cstring.hpp:21, from /usr/include/boost/test/detail/global_typedef.hpp:15, from /usr/include/boost/test/tree/observer.hpp:17, from /usr/include/boost/test/unit_test_log.hpp:18, from /usr/include/boost/test/tools/old/impl.hpp:19, from /usr/include/boost/test/test_tools.hpp:46, from /usr/include/boost/test/unit_test.hpp:18, from /build/reproducible-path/openstructure-2.3.1/modules/io/tests/test_io_img.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ . ---------------------------------------------------------------------- Ran 2 tests in 38.942s OK Could not find CAD score classic executables: ignoring unit tests make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 96%] Built target test_cadscore.py_run [ 96%] Linking CXX executable ../../../tests/ost_io_tests cd /build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/modules/io/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_io_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/reproducible-path/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -Wall -Wno-attributes -O3 -DNDEBUG -fno-strict-aliasing -Wl,-z,relro CMakeFiles/ost_io_tests.dir/test_clustal.cc.o CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o CMakeFiles/ost_io_tests.dir/test_pir.cc.o CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o CMakeFiles/ost_io_tests.dir/tests.cc.o CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o CMakeFiles/ost_io_tests.dir/test_io_img.cc.o CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o -o ../../../tests/ost_io_tests -L/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib -Wl,-rpath,/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu/stage/lib /usr/lib/i386-linux-gnu/libboost_unit_test_framework.so ../../../stage/lib/libost_io.so.2.3.1 ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/i386-linux-gnu/libsqlite3.so /usr/lib/i386-linux-gnu/libboost_program_options.so /usr/lib/i386-linux-gnu/libboost_thread.so /usr/lib/i386-linux-gnu/libboost_chrono.so /usr/lib/i386-linux-gnu/libboost_date_time.so /usr/lib/i386-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/i386-linux-gnu/libboost_filesystem.so /usr/lib/i386-linux-gnu/libboost_system.so /usr/lib/i386-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/i386-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/i386-linux-gnu/libfftw3f.so /usr/lib/i386-linux-gnu/libfftw3f_threads.so /usr/lib/i386-linux-gnu/libboost_iostreams.so /usr/lib/i386-linux-gnu/libboost_regex.so /usr/lib/i386-linux-gnu/libtiff.so /usr/lib/i386-linux-gnu/libpng.so /usr/lib/i386-linux-gnu/libz.so make[4]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' [ 96%] Built target ost_io_tests make[3]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[2]: *** [CMakeFiles/Makefile2:1581: CMakeFiles/check.dir/rule] Error 2 make[2]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' make[1]: *** [Makefile:192: check] Error 2 make[1]: Leaving directory '/build/reproducible-path/openstructure-2.3.1/obj-i686-linux-gnu' dh_auto_test: error: cd obj-i686-linux-gnu && make -j8 check ARGS\+=--verbose ARGS\+=-j8 returned exit code 2 make: *** [debian/rules:11: binary] Error 25 dpkg-buildpackage: error: debian/rules binary subprocess returned exit status 2 I: copying local configuration E: Failed autobuilding of package 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/31460 and its subdirectories