I: pbuilder: network access will be disabled during build I: Current time: Wed Jun 7 12:26:12 -12 2023 I: pbuilder-time-stamp: 1686183972 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: 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 Tue May 23 16:59:49 2023 -12 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/31568/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='arm64' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=8 ' DISTRIBUTION='bookworm' HOME='/var/lib/jenkins' HOST_ARCH='arm64' IFS=' ' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' 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='31568' 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.RjnxTv7j/pbuilderrc_hlY4 --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.RjnxTv7j/b1 --logfile b1/build.log openstructure_2.3.1-9.dsc' SUDO_GID='117' SUDO_UID='110' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' USERNAME='root' _='/usr/bin/systemd-run' http_proxy='http://192.168.101.16:3128' I: uname -a Linux codethink16-arm64 4.15.0-212-generic #223-Ubuntu SMP Tue May 23 13:09:17 UTC 2023 aarch64 GNU/Linux I: ls -l /bin lrwxrwxrwx 1 root root 7 Jun 4 22:24 /bin -> usr/bin I: user script /srv/workspace/pbuilder/31568/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: arm64 Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: clustalw, cmake, debhelper-compat (= 13), dh-python, dssp, libboost-all-dev, libeigen3-dev, libfftw3-dev, libglu1-mesa-dev, libopenmm-dev, libopenmm-plugins, 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 ... 19611 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 libopenmm-dev; however: Package libopenmm-dev is not installed. pbuilder-satisfydepends-dummy depends on libopenmm-plugins; however: Package libopenmm-plugins 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-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-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} libopenmm-dev{a} libopenmm-plugins{a} libopenmm7.7{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} 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} libucx0{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} 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 245 MB of archives. After unpacking 1346 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-minimal arm64 3.11.2-6 [806 kB] Get: 2 http://deb.debian.org/debian bookworm/main arm64 libexpat1 arm64 2.5.0-1 [84.8 kB] Get: 3 http://deb.debian.org/debian bookworm/main arm64 python3.11-minimal arm64 3.11.2-6 [1858 kB] Get: 4 http://deb.debian.org/debian bookworm/main arm64 python3-minimal arm64 3.11.2-1+b1 [26.3 kB] Get: 5 http://deb.debian.org/debian bookworm/main arm64 media-types all 10.0.0 [26.1 kB] Get: 6 http://deb.debian.org/debian bookworm/main arm64 readline-common all 8.2-1.3 [69.0 kB] Get: 7 http://deb.debian.org/debian bookworm/main arm64 libreadline8 arm64 8.2-1.3 [155 kB] Get: 8 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-stdlib arm64 3.11.2-6 [1747 kB] Get: 9 http://deb.debian.org/debian bookworm/main arm64 python3.11 arm64 3.11.2-6 [572 kB] Get: 10 http://deb.debian.org/debian bookworm/main arm64 libpython3-stdlib arm64 3.11.2-1+b1 [9296 B] Get: 11 http://deb.debian.org/debian bookworm/main arm64 python3 arm64 3.11.2-1+b1 [26.3 kB] Get: 12 http://deb.debian.org/debian bookworm/main arm64 libproc2-0 arm64 2:4.0.2-3 [60.1 kB] Get: 13 http://deb.debian.org/debian bookworm/main arm64 procps arm64 2:4.0.2-3 [698 kB] Get: 14 http://deb.debian.org/debian bookworm/main arm64 sensible-utils all 0.0.17+nmu1 [19.0 kB] Get: 15 http://deb.debian.org/debian bookworm/main arm64 libmagic-mgc arm64 1:5.44-3 [305 kB] Get: 16 http://deb.debian.org/debian bookworm/main arm64 libmagic1 arm64 1:5.44-3 [98.5 kB] Get: 17 http://deb.debian.org/debian bookworm/main arm64 file arm64 1:5.44-3 [42.5 kB] Get: 18 http://deb.debian.org/debian bookworm/main arm64 gettext-base arm64 0.21-12 [159 kB] Get: 19 http://deb.debian.org/debian bookworm/main arm64 libuchardet0 arm64 0.0.7-1 [67.9 kB] Get: 20 http://deb.debian.org/debian bookworm/main arm64 groff-base arm64 1.22.4-10 [861 kB] Get: 21 http://deb.debian.org/debian bookworm/main arm64 bsdextrautils arm64 2.38.1-5+b1 [86.9 kB] Get: 22 http://deb.debian.org/debian bookworm/main arm64 libpipeline1 arm64 1.5.7-1 [36.4 kB] Get: 23 http://deb.debian.org/debian bookworm/main arm64 man-db arm64 2.11.2-2 [1369 kB] Get: 24 http://deb.debian.org/debian bookworm/main arm64 libbsd0 arm64 0.11.7-2 [115 kB] Get: 25 http://deb.debian.org/debian bookworm/main arm64 libedit2 arm64 3.1-20221030-2 [88.1 kB] Get: 26 http://deb.debian.org/debian bookworm/main arm64 libcbor0.8 arm64 0.8.0-2+b1 [26.0 kB] Get: 27 http://deb.debian.org/debian bookworm/main arm64 libfido2-1 arm64 1.12.0-2+b1 [72.6 kB] Get: 28 http://deb.debian.org/debian bookworm/main arm64 openssh-client arm64 1:9.2p1-2 [931 kB] Get: 29 http://deb.debian.org/debian bookworm/main arm64 m4 arm64 1.4.19-3 [276 kB] Get: 30 http://deb.debian.org/debian bookworm/main arm64 autoconf all 2.71-3 [332 kB] Get: 31 http://deb.debian.org/debian bookworm/main arm64 autotools-dev all 20220109.1 [51.6 kB] Get: 32 http://deb.debian.org/debian bookworm/main arm64 automake all 1:1.16.5-1.3 [823 kB] Get: 33 http://deb.debian.org/debian bookworm/main arm64 autopoint all 0.21-12 [495 kB] Get: 34 http://deb.debian.org/debian bookworm/main arm64 libtcl8.6 arm64 8.6.13+dfsg-2 [973 kB] Get: 35 http://deb.debian.org/debian bookworm/main arm64 libbrotli1 arm64 1.0.9-2+b6 [269 kB] Get: 36 http://deb.debian.org/debian bookworm/main arm64 libpng16-16 arm64 1.6.39-2 [269 kB] Get: 37 http://deb.debian.org/debian bookworm/main arm64 libfreetype6 arm64 2.12.1+dfsg-5 [369 kB] Get: 38 http://deb.debian.org/debian bookworm/main arm64 fonts-dejavu-core all 2.37-6 [1068 kB] Get: 39 http://deb.debian.org/debian bookworm/main arm64 fontconfig-config arm64 2.14.1-4 [315 kB] Get: 40 http://deb.debian.org/debian bookworm/main arm64 libfontconfig1 arm64 2.14.1-4 [381 kB] Get: 41 http://deb.debian.org/debian bookworm/main arm64 libxau6 arm64 1:1.0.9-1 [19.7 kB] Get: 42 http://deb.debian.org/debian bookworm/main arm64 libxdmcp6 arm64 1:1.1.2-3 [25.4 kB] Get: 43 http://deb.debian.org/debian bookworm/main arm64 libxcb1 arm64 1.15-1 [143 kB] Get: 44 http://deb.debian.org/debian bookworm/main arm64 libx11-data all 2:1.8.4-2 [292 kB] Get: 45 http://deb.debian.org/debian bookworm/main arm64 libx11-6 arm64 2:1.8.4-2 [736 kB] Get: 46 http://deb.debian.org/debian bookworm/main arm64 libxrender1 arm64 1:0.9.10-1.1 [32.0 kB] Get: 47 http://deb.debian.org/debian bookworm/main arm64 libxft2 arm64 2.3.6-1 [58.7 kB] Get: 48 http://deb.debian.org/debian bookworm/main arm64 libxext6 arm64 2:1.3.4-1+b1 [51.7 kB] Get: 49 http://deb.debian.org/debian bookworm/main arm64 x11-common all 1:7.7+23 [252 kB] Get: 50 http://deb.debian.org/debian bookworm/main arm64 libxss1 arm64 1:1.2.3-1 [17.8 kB] Get: 51 http://deb.debian.org/debian bookworm/main arm64 libtk8.6 arm64 8.6.13-2 [729 kB] Get: 52 http://deb.debian.org/debian bookworm/main arm64 tk8.6-blt2.5 arm64 2.5.3+dfsg-4.1 [540 kB] Get: 53 http://deb.debian.org/debian bookworm/main arm64 blt arm64 2.5.3+dfsg-4.1 [14.9 kB] Get: 54 http://deb.debian.org/debian bookworm/main arm64 clustalw arm64 2.1+lgpl-7 [248 kB] Get: 55 http://deb.debian.org/debian bookworm/main arm64 libicu72 arm64 72.1-3 [9204 kB] Get: 56 http://deb.debian.org/debian bookworm/main arm64 libxml2 arm64 2.9.14+dfsg-1.2 [620 kB] Get: 57 http://deb.debian.org/debian bookworm/main arm64 libarchive13 arm64 3.6.2-1 [316 kB] Get: 58 http://deb.debian.org/debian bookworm/main arm64 libsasl2-modules-db arm64 2.1.28+dfsg-10 [20.8 kB] Get: 59 http://deb.debian.org/debian bookworm/main arm64 libsasl2-2 arm64 2.1.28+dfsg-10 [58.0 kB] Get: 60 http://deb.debian.org/debian bookworm/main arm64 libldap-2.5-0 arm64 2.5.13+dfsg-5 [171 kB] Get: 61 http://deb.debian.org/debian bookworm/main arm64 libnghttp2-14 arm64 1.52.0-1 [67.9 kB] Get: 62 http://deb.debian.org/debian bookworm/main arm64 libpsl5 arm64 0.21.2-1 [58.6 kB] Get: 63 http://deb.debian.org/debian bookworm/main arm64 librtmp1 arm64 2.4+20151223.gitfa8646d.1-2+b2 [59.4 kB] Get: 64 http://deb.debian.org/debian bookworm/main arm64 libssh2-1 arm64 1.10.0-3+b1 [172 kB] Get: 65 http://deb.debian.org/debian bookworm/main arm64 libcurl4 arm64 7.88.1-10 [362 kB] Get: 66 http://deb.debian.org/debian bookworm/main arm64 libjsoncpp25 arm64 1.9.5-4 [72.3 kB] Get: 67 http://deb.debian.org/debian bookworm/main arm64 librhash0 arm64 1.4.3-3 [131 kB] Get: 68 http://deb.debian.org/debian bookworm/main arm64 libuv1 arm64 1.44.2-1 [133 kB] Get: 69 http://deb.debian.org/debian bookworm/main arm64 cmake-data all 3.25.1-1 [2026 kB] Get: 70 http://deb.debian.org/debian bookworm/main arm64 cmake arm64 3.25.1-1 [6806 kB] Get: 71 http://deb.debian.org/debian bookworm/main arm64 libdebhelper-perl all 13.11.4 [81.2 kB] Get: 72 http://deb.debian.org/debian bookworm/main arm64 libtool all 2.4.7-5 [517 kB] Get: 73 http://deb.debian.org/debian bookworm/main arm64 dh-autoreconf all 20 [17.1 kB] Get: 74 http://deb.debian.org/debian bookworm/main arm64 libarchive-zip-perl all 1.68-1 [104 kB] Get: 75 http://deb.debian.org/debian bookworm/main arm64 libsub-override-perl all 0.09-4 [9304 B] Get: 76 http://deb.debian.org/debian bookworm/main arm64 libfile-stripnondeterminism-perl all 1.13.1-1 [19.4 kB] Get: 77 http://deb.debian.org/debian bookworm/main arm64 dh-strip-nondeterminism all 1.13.1-1 [8620 B] Get: 78 http://deb.debian.org/debian bookworm/main arm64 libelf1 arm64 0.188-2.1 [173 kB] Get: 79 http://deb.debian.org/debian bookworm/main arm64 dwz arm64 0.15-1 [101 kB] Get: 80 http://deb.debian.org/debian bookworm/main arm64 gettext arm64 0.21-12 [1248 kB] Get: 81 http://deb.debian.org/debian bookworm/main arm64 intltool-debian all 0.35.0+20060710.6 [22.9 kB] Get: 82 http://deb.debian.org/debian bookworm/main arm64 po-debconf all 1.0.21+nmu1 [248 kB] Get: 83 http://deb.debian.org/debian bookworm/main arm64 debhelper all 13.11.4 [942 kB] Get: 84 http://deb.debian.org/debian bookworm/main arm64 python3-lib2to3 all 3.11.2-3 [76.3 kB] Get: 85 http://deb.debian.org/debian bookworm/main arm64 python3-distutils all 3.11.2-3 [131 kB] Get: 86 http://deb.debian.org/debian bookworm/main arm64 dh-python all 5.20230130 [104 kB] Get: 87 http://deb.debian.org/debian bookworm/main arm64 libboost-regex1.74.0 arm64 1.74.0+ds1-21 [448 kB] Get: 88 http://deb.debian.org/debian bookworm/main arm64 libcifpp-data all 5.0.7.1-1 [452 kB] Get: 89 http://deb.debian.org/debian bookworm/main arm64 libcifpp5 arm64 5.0.7.1-1 [698 kB] Get: 90 http://deb.debian.org/debian bookworm/main arm64 dssp arm64 4.2.2-2 [603 kB] Get: 91 http://deb.debian.org/debian bookworm/main arm64 fontconfig arm64 2.14.1-4 [449 kB] Get: 92 http://deb.debian.org/debian bookworm/main arm64 fonts-lyx all 2.3.7-1 [186 kB] Get: 93 http://deb.debian.org/debian bookworm/main arm64 libgfortran5 arm64 12.2.0-14 [340 kB] Get: 94 http://deb.debian.org/debian bookworm/main arm64 libgfortran-12-dev arm64 12.2.0-14 [396 kB] Get: 95 http://deb.debian.org/debian bookworm/main arm64 gfortran-12 arm64 12.2.0-14 [8646 kB] Get: 96 http://deb.debian.org/debian bookworm/main arm64 libnl-3-200 arm64 3.7.0-0.2+b1 [60.2 kB] Get: 97 http://deb.debian.org/debian bookworm/main arm64 libnl-route-3-200 arm64 3.7.0-0.2+b1 [168 kB] Get: 98 http://deb.debian.org/debian bookworm/main arm64 libibverbs1 arm64 44.0-2 [56.8 kB] Get: 99 http://deb.debian.org/debian bookworm/main arm64 ibverbs-providers arm64 44.0-2 [306 kB] Get: 100 http://deb.debian.org/debian bookworm/main arm64 icu-devtools arm64 72.1-3 [192 kB] Get: 101 http://deb.debian.org/debian bookworm/main arm64 libavahi-common-data arm64 0.8-10 [107 kB] Get: 102 http://deb.debian.org/debian bookworm/main arm64 libavahi-common3 arm64 0.8-10 [40.6 kB] Get: 103 http://deb.debian.org/debian bookworm/main arm64 libdbus-1-3 arm64 1.14.6-1 [191 kB] Get: 104 http://deb.debian.org/debian bookworm/main arm64 libavahi-client3 arm64 0.8-10 [43.8 kB] Get: 105 http://deb.debian.org/debian bookworm/main arm64 libblas3 arm64 3.11.0-2 [91.4 kB] Get: 106 http://deb.debian.org/debian bookworm/main arm64 libboost1.74-dev arm64 1.74.0+ds1-21 [9508 kB] Get: 107 http://deb.debian.org/debian bookworm/main arm64 libboost-dev arm64 1.74.0.3 [4548 B] Get: 108 http://deb.debian.org/debian bookworm/main arm64 libboost1.74-tools-dev arm64 1.74.0+ds1-21 [1328 kB] Get: 109 http://deb.debian.org/debian bookworm/main arm64 libboost-tools-dev arm64 1.74.0.3 [4508 B] Get: 110 http://deb.debian.org/debian bookworm/main arm64 libboost-atomic1.74.0 arm64 1.74.0+ds1-21 [220 kB] Get: 111 http://deb.debian.org/debian bookworm/main arm64 libboost-atomic1.74-dev arm64 1.74.0+ds1-21 [221 kB] Get: 112 http://deb.debian.org/debian bookworm/main arm64 libboost-atomic-dev arm64 1.74.0.3 [4640 B] Get: 113 http://deb.debian.org/debian bookworm/main arm64 libboost-chrono1.74.0 arm64 1.74.0+ds1-21 [227 kB] Get: 114 http://deb.debian.org/debian bookworm/main arm64 libboost-chrono1.74-dev arm64 1.74.0+ds1-21 [235 kB] Get: 115 http://deb.debian.org/debian bookworm/main arm64 libboost-chrono-dev arm64 1.74.0.3 [4960 B] Get: 116 http://deb.debian.org/debian bookworm/main arm64 libboost-container1.74.0 arm64 1.74.0+ds1-21 [245 kB] Get: 117 http://deb.debian.org/debian bookworm/main arm64 libboost-container1.74-dev arm64 1.74.0+ds1-21 [251 kB] Get: 118 http://deb.debian.org/debian bookworm/main arm64 libboost-container-dev arm64 1.74.0.3 [4812 B] Get: 119 http://deb.debian.org/debian bookworm/main arm64 libboost-date-time1.74.0 arm64 1.74.0+ds1-21 [218 kB] Get: 120 http://deb.debian.org/debian bookworm/main arm64 libboost-serialization1.74.0 arm64 1.74.0+ds1-21 [308 kB] Get: 121 http://deb.debian.org/debian bookworm/main arm64 libboost-serialization1.74-dev arm64 1.74.0+ds1-21 [357 kB] Get: 122 http://deb.debian.org/debian bookworm/main arm64 libboost-date-time1.74-dev arm64 1.74.0+ds1-21 [226 kB] Get: 123 http://deb.debian.org/debian bookworm/main arm64 libboost-system1.74.0 arm64 1.74.0+ds1-21 [218 kB] Get: 124 http://deb.debian.org/debian bookworm/main arm64 libboost-system1.74-dev arm64 1.74.0+ds1-21 [219 kB] Get: 125 http://deb.debian.org/debian bookworm/main arm64 libboost-thread1.74.0 arm64 1.74.0+ds1-21 [253 kB] Get: 126 http://deb.debian.org/debian bookworm/main arm64 libboost-thread1.74-dev arm64 1.74.0+ds1-21 [267 kB] Get: 127 http://deb.debian.org/debian bookworm/main arm64 libboost-context1.74.0 arm64 1.74.0+ds1-21 [219 kB] Get: 128 http://deb.debian.org/debian bookworm/main arm64 libboost-context1.74-dev arm64 1.74.0+ds1-21 [220 kB] Get: 129 http://deb.debian.org/debian bookworm/main arm64 libboost-context-dev arm64 1.74.0.3 [4540 B] Get: 130 http://deb.debian.org/debian bookworm/main arm64 libboost-coroutine1.74.0 arm64 1.74.0+ds1-21 [233 kB] Get: 131 http://deb.debian.org/debian bookworm/main arm64 libboost-coroutine1.74-dev arm64 1.74.0+ds1-21 [243 kB] Get: 132 http://deb.debian.org/debian bookworm/main arm64 libboost-coroutine-dev arm64 1.74.0.3 [4608 B] Get: 133 http://deb.debian.org/debian bookworm/main arm64 libboost-date-time-dev arm64 1.74.0.3 [4332 B] Get: 134 http://deb.debian.org/debian bookworm/main arm64 libboost-exception1.74-dev arm64 1.74.0+ds1-21 [217 kB] Get: 135 http://deb.debian.org/debian bookworm/main arm64 libboost-exception-dev arm64 1.74.0.3 [4320 B] Get: 136 http://deb.debian.org/debian bookworm/main arm64 libboost-filesystem1.74.0 arm64 1.74.0+ds1-21 [254 kB] Get: 137 http://deb.debian.org/debian bookworm/main arm64 libboost-filesystem1.74-dev arm64 1.74.0+ds1-21 [277 kB] Get: 138 http://deb.debian.org/debian bookworm/main arm64 libboost-fiber1.74.0 arm64 1.74.0+ds1-21 [239 kB] Get: 139 http://deb.debian.org/debian bookworm/main arm64 libboost-fiber1.74-dev arm64 1.74.0+ds1-21 [252 kB] Get: 140 http://deb.debian.org/debian bookworm/main arm64 libboost-fiber-dev arm64 1.74.0.3 [4760 B] Get: 141 http://deb.debian.org/debian bookworm/main arm64 libboost-filesystem-dev arm64 1.74.0.3 [4368 B] Get: 142 http://deb.debian.org/debian bookworm/main arm64 libboost-graph1.74.0 arm64 1.74.0+ds1-21 [292 kB] Get: 143 http://deb.debian.org/debian bookworm/main arm64 libicu-dev arm64 72.1-3 [10.2 MB] Get: 144 http://deb.debian.org/debian bookworm/main arm64 libboost-regex1.74-dev arm64 1.74.0+ds1-21 [526 kB] Get: 145 http://deb.debian.org/debian bookworm/main arm64 libboost-test1.74.0 arm64 1.74.0+ds1-21 [423 kB] Get: 146 http://deb.debian.org/debian bookworm/main arm64 libboost-test1.74-dev arm64 1.74.0+ds1-21 [513 kB] Get: 147 http://deb.debian.org/debian bookworm/main arm64 libboost-graph1.74-dev arm64 1.74.0+ds1-21 [316 kB] Get: 148 http://deb.debian.org/debian bookworm/main arm64 libboost-graph-dev arm64 1.74.0.3 [4436 B] Get: 149 http://deb.debian.org/debian bookworm/main arm64 libevent-core-2.1-7 arm64 2.1.12-stable-8 [124 kB] Get: 150 http://deb.debian.org/debian bookworm/main arm64 libevent-pthreads-2.1-7 arm64 2.1.12-stable-8 [53.7 kB] Get: 151 http://deb.debian.org/debian bookworm/main arm64 librdmacm1 arm64 44.0-2 [64.9 kB] Get: 152 http://deb.debian.org/debian bookworm/main arm64 libfabric1 arm64 1.17.0-3 [476 kB] Get: 153 http://deb.debian.org/debian bookworm/main arm64 libhwloc15 arm64 2.9.0-1 [133 kB] Get: 154 http://deb.debian.org/debian bookworm/main arm64 libmunge2 arm64 0.5.15-2 [18.8 kB] Get: 155 http://deb.debian.org/debian bookworm/main arm64 libpciaccess0 arm64 0.17-2 [50.4 kB] Get: 156 http://deb.debian.org/debian bookworm/main arm64 libxnvctrl0 arm64 525.85.05-1 [13.3 kB] Get: 157 http://deb.debian.org/debian bookworm/main arm64 ocl-icd-libopencl1 arm64 2.3.1-1 [42.1 kB] Get: 158 http://deb.debian.org/debian bookworm/main arm64 libhwloc-plugins arm64 2.9.0-1 [17.2 kB] Get: 159 http://deb.debian.org/debian bookworm/main arm64 libpmix2 arm64 4.2.2-1+b1 [554 kB] Get: 160 http://deb.debian.org/debian bookworm/main arm64 libnuma1 arm64 2.0.16-1 [20.3 kB] Get: 161 http://deb.debian.org/debian bookworm/main arm64 libucx0 arm64 1.13.1-1 [734 kB] Get: 162 http://deb.debian.org/debian bookworm/main arm64 libopenmpi3 arm64 4.1.4-3+b1 [2161 kB] Get: 163 http://deb.debian.org/debian bookworm/main arm64 libboost-mpi1.74.0 arm64 1.74.0+ds1-21 [254 kB] Get: 164 http://deb.debian.org/debian bookworm/main arm64 libboost-graph-parallel1.74.0 arm64 1.74.0+ds1-21 [261 kB] Get: 165 http://deb.debian.org/debian bookworm/main arm64 libboost-graph-parallel1.74-dev arm64 1.74.0+ds1-21 [269 kB] Get: 166 http://deb.debian.org/debian bookworm/main arm64 libboost-graph-parallel-dev arm64 1.74.0.3 [4460 B] Get: 167 http://deb.debian.org/debian bookworm/main arm64 libboost-iostreams1.74-dev arm64 1.74.0+ds1-21 [247 kB] Get: 168 http://deb.debian.org/debian bookworm/main arm64 libboost-iostreams-dev arm64 1.74.0.3 [4316 B] Get: 169 http://deb.debian.org/debian bookworm/main arm64 libboost-locale1.74.0 arm64 1.74.0+ds1-21 [420 kB] Get: 170 http://deb.debian.org/debian bookworm/main arm64 libboost-locale1.74-dev arm64 1.74.0+ds1-21 [541 kB] Get: 171 http://deb.debian.org/debian bookworm/main arm64 libboost-locale-dev arm64 1.74.0.3 [4660 B] Get: 172 http://deb.debian.org/debian bookworm/main arm64 libboost-log1.74.0 arm64 1.74.0+ds1-21 [549 kB] Get: 173 http://deb.debian.org/debian bookworm/main arm64 libboost-log1.74-dev arm64 1.74.0+ds1-21 [770 kB] Get: 174 http://deb.debian.org/debian bookworm/main arm64 libboost-log-dev arm64 1.74.0.3 [4540 B] Get: 175 http://deb.debian.org/debian bookworm/main arm64 libboost-math1.74.0 arm64 1.74.0+ds1-21 [453 kB] Get: 176 http://deb.debian.org/debian bookworm/main arm64 libboost-math1.74-dev arm64 1.74.0+ds1-21 [543 kB] Get: 177 http://deb.debian.org/debian bookworm/main arm64 libboost-math-dev arm64 1.74.0.3 [4532 B] Get: 178 http://deb.debian.org/debian bookworm/main arm64 openmpi-common all 4.1.4-3 [167 kB] Get: 179 http://deb.debian.org/debian bookworm/main arm64 libnl-3-dev arm64 3.7.0-0.2+b1 [104 kB] Get: 180 http://deb.debian.org/debian bookworm/main arm64 libnl-route-3-dev arm64 3.7.0-0.2+b1 [200 kB] Get: 181 http://deb.debian.org/debian bookworm/main arm64 libibverbs-dev arm64 44.0-2 [613 kB] Get: 182 http://deb.debian.org/debian bookworm/main arm64 libnuma-dev arm64 2.0.16-1 [36.0 kB] Get: 183 http://deb.debian.org/debian bookworm/main arm64 libltdl7 arm64 2.4.7-5 [392 kB] Get: 184 http://deb.debian.org/debian bookworm/main arm64 libltdl-dev arm64 2.4.7-5 [165 kB] Get: 185 http://deb.debian.org/debian bookworm/main arm64 libhwloc-dev arm64 2.9.0-1 [734 kB] Get: 186 http://deb.debian.org/debian bookworm/main arm64 libevent-2.1-7 arm64 2.1.12-stable-8 [168 kB] Get: 187 http://deb.debian.org/debian bookworm/main arm64 libevent-extra-2.1-7 arm64 2.1.12-stable-8 [101 kB] Get: 188 http://deb.debian.org/debian bookworm/main arm64 libevent-openssl-2.1-7 arm64 2.1.12-stable-8 [59.7 kB] Get: 189 http://deb.debian.org/debian bookworm/main arm64 libevent-dev arm64 2.1.12-stable-8 [302 kB] Get: 190 http://deb.debian.org/debian bookworm/main arm64 zlib1g-dev arm64 1:1.2.13.dfsg-1 [913 kB] Get: 191 http://deb.debian.org/debian bookworm/main arm64 libpmix-dev arm64 4.2.2-1+b1 [883 kB] Get: 192 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery all 3.6.1+dfsg+~3.5.14-1 [326 kB] Get: 193 http://deb.debian.org/debian bookworm/main arm64 libjs-jquery-ui all 1.13.2+dfsg-1 [250 kB] Get: 194 http://deb.debian.org/debian bookworm/main arm64 openmpi-bin arm64 4.1.4-3+b1 [225 kB] Get: 195 http://deb.debian.org/debian bookworm/main arm64 libopenmpi-dev arm64 4.1.4-3+b1 [970 kB] Get: 196 http://deb.debian.org/debian bookworm/main arm64 mpi-default-dev arm64 1.14 [5548 B] Get: 197 http://deb.debian.org/debian bookworm/main arm64 libboost-mpi1.74-dev arm64 1.74.0+ds1-21 [277 kB] Get: 198 http://deb.debian.org/debian bookworm/main arm64 libboost-mpi-dev arm64 1.74.0.3 [4420 B] Get: 199 http://deb.debian.org/debian bookworm/main arm64 libboost-python1.74.0 arm64 1.74.0+ds1-21 [281 kB] Get: 200 http://deb.debian.org/debian bookworm/main arm64 mpi-default-bin arm64 1.14 [4752 B] Get: 201 http://deb.debian.org/debian bookworm/main arm64 libboost-mpi-python1.74.0 arm64 1.74.0+ds1-21 [328 kB] Get: 202 http://deb.debian.org/debian bookworm/main arm64 libboost-mpi-python1.74-dev arm64 1.74.0+ds1-21 [224 kB] Get: 203 http://deb.debian.org/debian bookworm/main arm64 libboost-mpi-python-dev arm64 1.74.0.3 [4456 B] Get: 204 http://deb.debian.org/debian bookworm/main arm64 libboost-numpy1.74.0 arm64 1.74.0+ds1-21 [228 kB] Get: 205 http://deb.debian.org/debian bookworm/main arm64 libboost-numpy1.74-dev arm64 1.74.0+ds1-21 [232 kB] Get: 206 http://deb.debian.org/debian bookworm/main arm64 libboost-numpy-dev arm64 1.74.0.3 [4376 B] Get: 207 http://deb.debian.org/debian bookworm/main arm64 libboost-program-options1.74.0 arm64 1.74.0+ds1-21 [317 kB] Get: 208 http://deb.debian.org/debian bookworm/main arm64 libboost-program-options1.74-dev arm64 1.74.0+ds1-21 [354 kB] Get: 209 http://deb.debian.org/debian bookworm/main arm64 libboost-program-options-dev arm64 1.74.0.3 [4340 B] Get: 210 http://deb.debian.org/debian bookworm/main arm64 libpython3.11 arm64 3.11.2-6 [1841 kB] Get: 211 http://deb.debian.org/debian bookworm/main arm64 libexpat1-dev arm64 2.5.0-1 [135 kB] Get: 212 http://deb.debian.org/debian bookworm/main arm64 libpython3.11-dev arm64 3.11.2-6 [4395 kB] Get: 213 http://deb.debian.org/debian bookworm/main arm64 libpython3-dev arm64 3.11.2-1+b1 [9564 B] Get: 214 http://deb.debian.org/debian bookworm/main arm64 python3.11-dev arm64 3.11.2-6 [617 kB] Get: 215 http://deb.debian.org/debian bookworm/main arm64 libjs-underscore all 1.13.4~dfsg+~1.11.4-3 [116 kB] Get: 216 http://deb.debian.org/debian bookworm/main arm64 libjs-sphinxdoc all 5.3.0-4 [130 kB] Get: 217 http://deb.debian.org/debian bookworm/main arm64 python3-dev arm64 3.11.2-1+b1 [26.2 kB] Get: 218 http://deb.debian.org/debian bookworm/main arm64 libboost-python1.74-dev arm64 1.74.0+ds1-21 [305 kB] Get: 219 http://deb.debian.org/debian bookworm/main arm64 libboost-python-dev arm64 1.74.0.3 [4632 B] Get: 220 http://deb.debian.org/debian bookworm/main arm64 libboost-random1.74.0 arm64 1.74.0+ds1-21 [226 kB] Get: 221 http://deb.debian.org/debian bookworm/main arm64 libboost-random1.74-dev arm64 1.74.0+ds1-21 [229 kB] Get: 222 http://deb.debian.org/debian bookworm/main arm64 libboost-random-dev arm64 1.74.0.3 [4336 B] Get: 223 http://deb.debian.org/debian bookworm/main arm64 libboost-regex-dev arm64 1.74.0.3 [4596 B] Get: 224 http://deb.debian.org/debian bookworm/main arm64 libboost-serialization-dev arm64 1.74.0.3 [4560 B] Get: 225 http://deb.debian.org/debian bookworm/main arm64 libboost-stacktrace1.74.0 arm64 1.74.0+ds1-21 [255 kB] Get: 226 http://deb.debian.org/debian bookworm/main arm64 libboost-stacktrace1.74-dev arm64 1.74.0+ds1-21 [231 kB] Get: 227 http://deb.debian.org/debian bookworm/main arm64 libboost-stacktrace-dev arm64 1.74.0.3 [4328 B] Get: 228 http://deb.debian.org/debian bookworm/main arm64 libboost-system-dev arm64 1.74.0.3 [4468 B] Get: 229 http://deb.debian.org/debian bookworm/main arm64 libboost-test-dev arm64 1.74.0.3 [4368 B] Get: 230 http://deb.debian.org/debian bookworm/main arm64 libboost-thread-dev arm64 1.74.0.3 [4356 B] Get: 231 http://deb.debian.org/debian bookworm/main arm64 libboost-timer1.74.0 arm64 1.74.0+ds1-21 [226 kB] Get: 232 http://deb.debian.org/debian bookworm/main arm64 libboost-timer1.74-dev arm64 1.74.0+ds1-21 [230 kB] Get: 233 http://deb.debian.org/debian bookworm/main arm64 libboost-timer-dev arm64 1.74.0.3 [4456 B] Get: 234 http://deb.debian.org/debian bookworm/main arm64 libboost-type-erasure1.74.0 arm64 1.74.0+ds1-21 [231 kB] Get: 235 http://deb.debian.org/debian bookworm/main arm64 libboost-type-erasure1.74-dev arm64 1.74.0+ds1-21 [236 kB] Get: 236 http://deb.debian.org/debian bookworm/main arm64 libboost-type-erasure-dev arm64 1.74.0.3 [4428 B] Get: 237 http://deb.debian.org/debian bookworm/main arm64 libboost-wave1.74.0 arm64 1.74.0+ds1-21 [396 kB] Get: 238 http://deb.debian.org/debian bookworm/main arm64 libboost-wave1.74-dev arm64 1.74.0+ds1-21 [477 kB] Get: 239 http://deb.debian.org/debian bookworm/main arm64 libboost-wave-dev arm64 1.74.0.3 [4360 B] Get: 240 http://deb.debian.org/debian bookworm/main arm64 libboost-nowide1.74.0 arm64 1.74.0+ds1-21 [219 kB] Get: 241 http://deb.debian.org/debian bookworm/main arm64 libboost-nowide1.74-dev arm64 1.74.0+ds1-21 [220 kB] Get: 242 http://deb.debian.org/debian bookworm/main arm64 libboost-nowide-dev arm64 1.74.0.3 [4392 B] Get: 243 http://deb.debian.org/debian bookworm/main arm64 libboost-all-dev arm64 1.74.0.3 [4680 B] Get: 244 http://deb.debian.org/debian bookworm/main arm64 libcups2 arm64 2.4.2-3 [228 kB] Get: 245 http://deb.debian.org/debian bookworm/main arm64 libdeflate0 arm64 1.14-1 [54.3 kB] Get: 246 http://deb.debian.org/debian bookworm/main arm64 libdeflate-dev arm64 1.14-1 [50.0 kB] Get: 247 http://deb.debian.org/debian bookworm/main arm64 libdouble-conversion3 arm64 3.2.1-1 [37.6 kB] Get: 248 http://deb.debian.org/debian bookworm/main arm64 libdrm-common all 2.4.114-1 [7112 B] Get: 249 http://deb.debian.org/debian bookworm/main arm64 libdrm2 arm64 2.4.114-1+b1 [36.7 kB] Get: 250 http://deb.debian.org/debian bookworm/main arm64 libdrm-amdgpu1 arm64 2.4.114-1+b1 [20.4 kB] Get: 251 http://deb.debian.org/debian bookworm/main arm64 libdrm-nouveau2 arm64 2.4.114-1+b1 [18.4 kB] Get: 252 http://deb.debian.org/debian bookworm/main arm64 libdrm-radeon1 arm64 2.4.114-1+b1 [20.9 kB] Get: 253 http://deb.debian.org/debian bookworm/main arm64 libglvnd0 arm64 1.6.0-1 [41.4 kB] Get: 254 http://deb.debian.org/debian bookworm/main arm64 libwayland-server0 arm64 1.21.0-1 [34.9 kB] Get: 255 http://deb.debian.org/debian bookworm/main arm64 libgbm1 arm64 22.3.6-1+deb12u1 [37.0 kB] Get: 256 http://deb.debian.org/debian bookworm/main arm64 libglapi-mesa arm64 22.3.6-1+deb12u1 [44.7 kB] Get: 257 http://deb.debian.org/debian bookworm/main arm64 libwayland-client0 arm64 1.21.0-1 [27.6 kB] Get: 258 http://deb.debian.org/debian bookworm/main arm64 libx11-xcb1 arm64 2:1.8.4-2 [192 kB] Get: 259 http://deb.debian.org/debian bookworm/main arm64 libxcb-dri2-0 arm64 1.15-1 [107 kB] Get: 260 http://deb.debian.org/debian bookworm/main arm64 libxcb-dri3-0 arm64 1.15-1 [107 kB] Get: 261 http://deb.debian.org/debian bookworm/main arm64 libxcb-present0 arm64 1.15-1 [106 kB] Get: 262 http://deb.debian.org/debian bookworm/main arm64 libxcb-randr0 arm64 1.15-1 [117 kB] Get: 263 http://deb.debian.org/debian bookworm/main arm64 libxcb-sync1 arm64 1.15-1 [109 kB] Get: 264 http://deb.debian.org/debian bookworm/main arm64 libxcb-xfixes0 arm64 1.15-1 [110 kB] Get: 265 http://deb.debian.org/debian bookworm/main arm64 libxshmfence1 arm64 1.3-1 [8712 B] Get: 266 http://deb.debian.org/debian bookworm/main arm64 libegl-mesa0 arm64 22.3.6-1+deb12u1 [107 kB] Get: 267 http://deb.debian.org/debian bookworm/main arm64 libegl1 arm64 1.6.0-1 [33.1 kB] Get: 268 http://deb.debian.org/debian bookworm/main arm64 libxcb-glx0 arm64 1.15-1 [123 kB] Get: 269 http://deb.debian.org/debian bookworm/main arm64 libxcb-shm0 arm64 1.15-1 [106 kB] Get: 270 http://deb.debian.org/debian bookworm/main arm64 libxfixes3 arm64 1:6.0.0-2 [22.9 kB] Get: 271 http://deb.debian.org/debian bookworm/main arm64 libxxf86vm1 arm64 1:1.1.4-1+b2 [20.1 kB] Get: 272 http://deb.debian.org/debian bookworm/main arm64 libz3-4 arm64 4.8.12-3.1 [6282 kB] Get: 273 http://deb.debian.org/debian bookworm/main arm64 libllvm15 arm64 1:15.0.6-4+b1 [20.7 MB] Get: 274 http://deb.debian.org/debian bookworm/main arm64 libsensors-config all 1:3.6.0-7.1 [14.3 kB] Get: 275 http://deb.debian.org/debian bookworm/main arm64 libsensors5 arm64 1:3.6.0-7.1 [33.3 kB] Get: 276 http://deb.debian.org/debian bookworm/main arm64 libgl1-mesa-dri arm64 22.3.6-1+deb12u1 [6278 kB] Get: 277 http://deb.debian.org/debian bookworm/main arm64 libglx-mesa0 arm64 22.3.6-1+deb12u1 [146 kB] Get: 278 http://deb.debian.org/debian bookworm/main arm64 libglx0 arm64 1.6.0-1 [30.8 kB] Get: 279 http://deb.debian.org/debian bookworm/main arm64 libgl1 arm64 1.6.0-1 [90.2 kB] Get: 280 http://deb.debian.org/debian bookworm/main arm64 xorg-sgml-doctools all 1:1.11-1.1 [22.1 kB] Get: 281 http://deb.debian.org/debian bookworm/main arm64 x11proto-dev all 2022.1-1 [599 kB] Get: 282 http://deb.debian.org/debian bookworm/main arm64 libxau-dev arm64 1:1.0.9-1 [23.2 kB] Get: 283 http://deb.debian.org/debian bookworm/main arm64 libxdmcp-dev arm64 1:1.1.2-3 [41.2 kB] Get: 284 http://deb.debian.org/debian bookworm/main arm64 xtrans-dev all 1.4.0-1 [98.7 kB] Get: 285 http://deb.debian.org/debian bookworm/main arm64 libpthread-stubs0-dev arm64 0.4-1 [5336 B] Get: 286 http://deb.debian.org/debian bookworm/main arm64 libxcb1-dev arm64 1.15-1 [182 kB] Get: 287 http://deb.debian.org/debian bookworm/main arm64 libx11-dev arm64 2:1.8.4-2 [817 kB] Get: 288 http://deb.debian.org/debian bookworm/main arm64 libglx-dev arm64 1.6.0-1 [15.3 kB] Get: 289 http://deb.debian.org/debian bookworm/main arm64 libgl-dev arm64 1.6.0-1 [100 kB] Get: 290 http://deb.debian.org/debian bookworm/main arm64 libegl-dev arm64 1.6.0-1 [19.1 kB] Get: 291 http://deb.debian.org/debian bookworm/main arm64 libpkgconf3 arm64 1.8.1-1 [35.3 kB] Get: 292 http://deb.debian.org/debian bookworm/main arm64 pkgconf-bin arm64 1.8.1-1 [28.9 kB] Get: 293 http://deb.debian.org/debian bookworm/main arm64 pkgconf arm64 1.8.1-1 [25.9 kB] Get: 294 http://deb.debian.org/debian bookworm/main arm64 pkg-config arm64 1.8.1-1 [13.7 kB] Get: 295 http://deb.debian.org/debian bookworm/main arm64 libeigen3-dev all 3.4.0-4 [1041 kB] Get: 296 http://deb.debian.org/debian bookworm/main arm64 libevdev2 arm64 1.13.0+dfsg-1 [32.0 kB] Get: 297 http://deb.debian.org/debian bookworm/main arm64 libfftw3-double3 arm64 3.3.10-1 [326 kB] Get: 298 http://deb.debian.org/debian bookworm/main arm64 libfftw3-long3 arm64 3.3.10-1 [529 kB] Get: 299 http://deb.debian.org/debian bookworm/main arm64 libfftw3-single3 arm64 3.3.10-1 [494 kB] Get: 300 http://deb.debian.org/debian bookworm/main arm64 libfftw3-bin arm64 3.3.10-1 [42.9 kB] Get: 301 http://deb.debian.org/debian bookworm/main arm64 libfftw3-dev arm64 3.3.10-1 [1186 kB] Get: 302 http://deb.debian.org/debian bookworm/main arm64 libfribidi0 arm64 1.0.8-2.1 [64.9 kB] Get: 303 http://deb.debian.org/debian bookworm/main arm64 libglib2.0-0 arm64 2.74.6-2 [1310 kB] Get: 304 http://deb.debian.org/debian bookworm/main arm64 libopengl0 arm64 1.6.0-1 [31.7 kB] Get: 305 http://deb.debian.org/debian bookworm/main arm64 libglu1-mesa arm64 9.0.2-1.1 [153 kB] Get: 306 http://deb.debian.org/debian bookworm/main arm64 libopengl-dev arm64 1.6.0-1 [4932 B] Get: 307 http://deb.debian.org/debian bookworm/main arm64 libglu1-mesa-dev arm64 9.0.2-1.1 [193 kB] Get: 308 http://deb.debian.org/debian bookworm/main arm64 libgraphite2-3 arm64 1.3.14-1 [75.6 kB] Get: 309 http://deb.debian.org/debian bookworm/main arm64 libgudev-1.0-0 arm64 237-2 [14.3 kB] Get: 310 http://deb.debian.org/debian bookworm/main arm64 libharfbuzz0b arm64 6.0.0+dfsg-3 [1914 kB] Get: 311 http://deb.debian.org/debian bookworm/main arm64 libice6 arm64 2:1.0.10-1 [55.6 kB] Get: 312 http://deb.debian.org/debian bookworm/main arm64 libimagequant0 arm64 2.17.0-1 [31.3 kB] Get: 313 http://deb.debian.org/debian bookworm/main arm64 libwacom-common all 2.6.0-1 [58.4 kB] Get: 314 http://deb.debian.org/debian bookworm/main arm64 libwacom9 arm64 2.6.0-1 [20.7 kB] Get: 315 http://deb.debian.org/debian bookworm/main arm64 libinput-bin arm64 1.22.1-1 [23.0 kB] Get: 316 http://deb.debian.org/debian bookworm/main arm64 libmtdev1 arm64 1.1.6-1 [22.8 kB] Get: 317 http://deb.debian.org/debian bookworm/main arm64 libinput10 arm64 1.22.1-1 [112 kB] Get: 318 http://deb.debian.org/debian bookworm/main arm64 libjbig0 arm64 2.1-6.1 [30.0 kB] Get: 319 http://deb.debian.org/debian bookworm/main arm64 libjbig-dev arm64 2.1-6.1 [29.9 kB] Get: 320 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo arm64 1:2.1.5-2 [171 kB] Get: 321 http://deb.debian.org/debian bookworm/main arm64 libjpeg62-turbo-dev arm64 1:2.1.5-2 [292 kB] Get: 322 http://deb.debian.org/debian bookworm/main arm64 libjpeg-dev arm64 1:2.1.5-2 [71.8 kB] Get: 323 http://deb.debian.org/debian bookworm/main arm64 libopenblas0-pthread arm64 0.3.21+ds-4 [4532 kB] Get: 324 http://deb.debian.org/debian bookworm/main arm64 liblapack3 arm64 3.11.0-2 [1664 kB] Get: 325 http://deb.debian.org/debian bookworm/main arm64 liblbfgsb0 arm64 3.0+dfsg.4-1 [24.9 kB] Get: 326 http://deb.debian.org/debian bookworm/main arm64 liblcms2-2 arm64 2.14-2 [143 kB] Get: 327 http://deb.debian.org/debian bookworm/main arm64 liblerc4 arm64 4.0.0+ds-2 [138 kB] Get: 328 http://deb.debian.org/debian bookworm/main arm64 liblerc-dev arm64 4.0.0+ds-2 [146 kB] Get: 329 http://deb.debian.org/debian bookworm/main arm64 liblzma-dev arm64 5.4.1-0.2 [255 kB] Get: 330 http://deb.debian.org/debian bookworm/main arm64 libmd4c0 arm64 0.4.8-1 [41.6 kB] Get: 331 http://deb.debian.org/debian bookworm/main arm64 libopenblas0 arm64 0.3.21+ds-4 [32.6 kB] Get: 332 http://deb.debian.org/debian bookworm/main arm64 libopenblas-pthread-dev arm64 0.3.21+ds-4 [3169 kB] Get: 333 http://deb.debian.org/debian bookworm/main arm64 libopenblas-dev arm64 0.3.21+ds-4 [44.9 kB] Get: 334 http://deb.debian.org/debian bookworm/main arm64 libopenjp2-7 arm64 2.5.0-2 [175 kB] Get: 335 http://deb.debian.org/debian bookworm/main arm64 libopenmm7.7 arm64 7.7.0+dfsg-9+b1 [632 kB] Get: 336 http://deb.debian.org/debian bookworm/main arm64 libopenmm-dev arm64 7.7.0+dfsg-9+b1 [313 kB] Get: 337 http://deb.debian.org/debian bookworm/main arm64 libopenmm-plugins arm64 7.7.0+dfsg-9+b1 [912 kB] Get: 338 http://deb.debian.org/debian bookworm/main arm64 libpcre2-16-0 arm64 10.42-1 [216 kB] Get: 339 http://deb.debian.org/debian bookworm/main arm64 libpng-dev arm64 1.6.39-2 [354 kB] Get: 340 http://deb.debian.org/debian bookworm/main arm64 libpython3-all-dev arm64 3.11.2-1+b1 [1068 B] Get: 341 http://deb.debian.org/debian bookworm/main arm64 libqhull-r8.0 arm64 2020.2-5 [230 kB] Get: 342 http://deb.debian.org/debian bookworm/main arm64 shared-mime-info arm64 2.2-1 [727 kB] Get: 343 http://deb.debian.org/debian bookworm/main arm64 libqt5core5a arm64 5.15.8+dfsg-11 [1661 kB] Get: 344 http://deb.debian.org/debian bookworm/main arm64 libqt5concurrent5 arm64 5.15.8+dfsg-11 [41.9 kB] Get: 345 http://deb.debian.org/debian bookworm/main arm64 libqt5dbus5 arm64 5.15.8+dfsg-11 [202 kB] Get: 346 http://deb.debian.org/debian bookworm/main arm64 libqt5network5 arm64 5.15.8+dfsg-11 [647 kB] Get: 347 http://deb.debian.org/debian bookworm/main arm64 libsm6 arm64 2:1.2.3-1 [34.0 kB] Get: 348 http://deb.debian.org/debian bookworm/main arm64 libxcb-icccm4 arm64 0.4.1-1.1 [26.9 kB] Get: 349 http://deb.debian.org/debian bookworm/main arm64 libxcb-util1 arm64 0.4.0-1+b1 [23.2 kB] Get: 350 http://deb.debian.org/debian bookworm/main arm64 libxcb-image0 arm64 0.4.0-2 [22.4 kB] Get: 351 http://deb.debian.org/debian bookworm/main arm64 libxcb-keysyms1 arm64 0.4.0-1+b2 [16.0 kB] Get: 352 http://deb.debian.org/debian bookworm/main arm64 libxcb-render0 arm64 1.15-1 [115 kB] Get: 353 http://deb.debian.org/debian bookworm/main arm64 libxcb-render-util0 arm64 0.3.9-1+b1 [17.5 kB] Get: 354 http://deb.debian.org/debian bookworm/main arm64 libxcb-shape0 arm64 1.15-1 [106 kB] Get: 355 http://deb.debian.org/debian bookworm/main arm64 libxcb-xinerama0 arm64 1.15-1 [105 kB] Get: 356 http://deb.debian.org/debian bookworm/main arm64 libxcb-xinput0 arm64 1.15-1 [130 kB] Get: 357 http://deb.debian.org/debian bookworm/main arm64 libxcb-xkb1 arm64 1.15-1 [128 kB] Get: 358 http://deb.debian.org/debian bookworm/main arm64 xkb-data all 2.35.1-1 [764 kB] Get: 359 http://deb.debian.org/debian bookworm/main arm64 libxkbcommon0 arm64 1.5.0-1 [100 kB] Get: 360 http://deb.debian.org/debian bookworm/main arm64 libxkbcommon-x11-0 arm64 1.5.0-1 [14.6 kB] Get: 361 http://deb.debian.org/debian bookworm/main arm64 libqt5gui5 arm64 5.15.8+dfsg-11 [3073 kB] Get: 362 http://deb.debian.org/debian bookworm/main arm64 libqt5widgets5 arm64 5.15.8+dfsg-11 [2257 kB] Get: 363 http://deb.debian.org/debian bookworm/main arm64 libqt5xml5 arm64 5.15.8+dfsg-11 [118 kB] Get: 364 http://deb.debian.org/debian bookworm/main arm64 libqt5designer5 arm64 5.15.8-2 [2713 kB] Get: 365 http://deb.debian.org/debian bookworm/main arm64 libqt5sql5 arm64 5.15.8+dfsg-11 [118 kB] Get: 366 http://deb.debian.org/debian bookworm/main arm64 libqt5help5 arm64 5.15.8-2 [143 kB] Get: 367 http://deb.debian.org/debian bookworm/main arm64 libqt5opengl5 arm64 5.15.8+dfsg-11 [140 kB] Get: 368 http://deb.debian.org/debian bookworm/main arm64 libqt5printsupport5 arm64 5.15.8+dfsg-11 [195 kB] Get: 369 http://deb.debian.org/debian bookworm/main arm64 libqt5test5 arm64 5.15.8+dfsg-11 [135 kB] Get: 370 http://deb.debian.org/debian bookworm/main arm64 libvulkan1 arm64 1.3.239.0-1 [111 kB] Get: 371 http://deb.debian.org/debian bookworm/main arm64 libvulkan-dev arm64 1.3.239.0-1 [1115 kB] Get: 372 http://deb.debian.org/debian bookworm/main arm64 libxext-dev arm64 2:1.3.4-1+b1 [107 kB] Get: 373 http://deb.debian.org/debian bookworm/main arm64 qt5-qmake-bin arm64 5.15.8+dfsg-11 [888 kB] Get: 374 http://deb.debian.org/debian bookworm/main arm64 qtchooser arm64 66-2 [24.9 kB] Get: 375 http://deb.debian.org/debian bookworm/main arm64 qt5-qmake arm64 5.15.8+dfsg-11 [221 kB] Get: 376 http://deb.debian.org/debian bookworm/main arm64 qtbase5-dev-tools arm64 5.15.8+dfsg-11 [708 kB] Get: 377 http://deb.debian.org/debian bookworm/main arm64 qtbase5-dev arm64 5.15.8+dfsg-11 [1118 kB] Get: 378 http://deb.debian.org/debian bookworm/main arm64 libqt5opengl5-dev arm64 5.15.8+dfsg-11 [49.0 kB] Get: 379 http://deb.debian.org/debian bookworm/main arm64 libraqm0 arm64 0.7.0-4.1 [10.4 kB] Get: 380 http://deb.debian.org/debian bookworm/main arm64 libsqlite3-dev arm64 3.40.1-2 [979 kB] Get: 381 http://deb.debian.org/debian bookworm/main arm64 libzstd-dev arm64 1.5.4+dfsg2-5 [317 kB] Get: 382 http://deb.debian.org/debian bookworm/main arm64 libwebp7 arm64 1.2.4-0.2 [259 kB] Get: 383 http://deb.debian.org/debian bookworm/main arm64 libwebpmux3 arm64 1.2.4-0.2 [109 kB] Get: 384 http://deb.debian.org/debian bookworm/main arm64 libwebpdemux2 arm64 1.2.4-0.2 [99.2 kB] Get: 385 http://deb.debian.org/debian bookworm/main arm64 libwebp-dev arm64 1.2.4-0.2 [376 kB] Get: 386 http://deb.debian.org/debian bookworm/main arm64 libtiff6 arm64 4.5.0-6 [300 kB] Get: 387 http://deb.debian.org/debian bookworm/main arm64 libtiffxx6 arm64 4.5.0-6 [144 kB] Get: 388 http://deb.debian.org/debian bookworm/main arm64 libtiff-dev arm64 4.5.0-6 [441 kB] Get: 389 http://deb.debian.org/debian bookworm/main arm64 libxsimd-dev arm64 8.1.0-7 [88.8 kB] Get: 390 http://deb.debian.org/debian bookworm/main arm64 libxslt1.1 arm64 1.1.35-1 [231 kB] Get: 391 http://deb.debian.org/debian bookworm/main arm64 python-matplotlib-data all 3.6.3-1 [2744 kB] Get: 392 http://deb.debian.org/debian bookworm/main arm64 python3-all arm64 3.11.2-1+b1 [1064 B] Get: 393 http://deb.debian.org/debian bookworm/main arm64 python3-all-dev arm64 3.11.2-1+b1 [1076 B] Get: 394 http://deb.debian.org/debian bookworm/main arm64 python3-appdirs all 1.4.4-3 [13.0 kB] Get: 395 http://deb.debian.org/debian bookworm/main arm64 python3-attr all 22.2.0-1 [65.4 kB] Get: 396 http://deb.debian.org/debian bookworm/main arm64 python3-gast all 0.5.2-2 [9364 B] Get: 397 http://deb.debian.org/debian bookworm/main arm64 python3-beniget all 0.4.1-3 [9920 B] Get: 398 http://deb.debian.org/debian bookworm/main arm64 python3-brotli arm64 1.0.9-2+b6 [281 kB] Get: 399 http://deb.debian.org/debian bookworm/main arm64 python3-pkg-resources all 66.1.1-1 [296 kB] Get: 400 http://deb.debian.org/debian bookworm/main arm64 python3-numpy arm64 1:1.24.2-1 [4751 kB] Get: 401 http://deb.debian.org/debian bookworm/main arm64 python3-contourpy arm64 1.0.7-1+b1 [154 kB] Get: 402 http://deb.debian.org/debian bookworm/main arm64 python3-cycler all 0.11.0-1 [8020 B] Get: 403 http://deb.debian.org/debian bookworm/main arm64 python3-six all 1.16.0-4 [17.5 kB] Get: 404 http://deb.debian.org/debian bookworm/main arm64 python3-dateutil all 2.8.2-2 [78.3 kB] Get: 405 http://deb.debian.org/debian bookworm/main arm64 python3-decorator all 5.1.1-3 [14.9 kB] Get: 406 http://deb.debian.org/debian bookworm/main arm64 python3-ply all 3.11-5 [65.8 kB] Get: 407 http://deb.debian.org/debian bookworm/main arm64 python3-pythran arm64 0.11.0+ds-7 [427 kB] Get: 408 http://deb.debian.org/debian bookworm/main arm64 python3-scipy arm64 1.10.1-2 [14.2 MB] Get: 409 http://deb.debian.org/debian bookworm/main arm64 python3-ufolib2 all 0.14.0+dfsg1-1 [34.3 kB] Get: 410 http://deb.debian.org/debian bookworm/main arm64 python3-mpmath all 1.2.1-2 [418 kB] Get: 411 http://deb.debian.org/debian bookworm/main arm64 python3-sympy all 1.11.1-1 [4358 kB] Get: 412 http://deb.debian.org/debian bookworm/main arm64 python3-tz all 2022.7.1-4 [30.1 kB] Get: 413 http://deb.debian.org/debian bookworm/main arm64 python3-fs all 2.4.16-2 [95.2 kB] Get: 414 http://deb.debian.org/debian bookworm/main arm64 python3-lxml arm64 4.9.2-1+b1 [1074 kB] Get: 415 http://deb.debian.org/debian bookworm/main arm64 python3-lz4 arm64 4.0.2+dfsg-1+b2 [25.0 kB] Get: 416 http://deb.debian.org/debian bookworm/main arm64 unicode-data all 15.0.0-1 [7984 kB] Get: 417 http://deb.debian.org/debian bookworm/main arm64 python3-fonttools arm64 4.38.0-1+b1 [990 kB] Get: 418 http://deb.debian.org/debian bookworm/main arm64 python3-kiwisolver arm64 1.4.4-1+b1 [55.4 kB] Get: 419 http://deb.debian.org/debian bookworm/main arm64 python3-pil arm64 9.4.0-1.1+b1 [452 kB] Get: 420 http://deb.debian.org/debian bookworm/main arm64 python3-tk arm64 3.11.2-3 [97.7 kB] Get: 421 http://deb.debian.org/debian bookworm/main arm64 python3-pil.imagetk arm64 9.4.0-1.1+b1 [74.4 kB] Get: 422 http://deb.debian.org/debian bookworm/main arm64 python3-pyparsing all 3.0.9-1 [138 kB] Get: 423 http://deb.debian.org/debian bookworm/main arm64 python3-packaging all 23.0-1 [32.5 kB] Get: 424 http://deb.debian.org/debian bookworm/main arm64 python3-matplotlib arm64 3.6.3-1+b1 [6774 kB] Get: 425 http://deb.debian.org/debian bookworm/main arm64 python3-pyqt5.sip arm64 12.11.1-1 [55.0 kB] Get: 426 http://deb.debian.org/debian bookworm/main arm64 python3-pyqt5 arm64 5.15.9+dfsg-1 [2281 kB] Get: 427 http://deb.debian.org/debian bookworm/main arm64 sip-dev arm64 4.19.25+dfsg-5+b1 [234 kB] Get: 428 http://deb.debian.org/debian bookworm/main arm64 voronota arm64 1.22.3149-2 [1919 kB] Fetched 245 MB in 24s (10.1 MB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libpython3.11-minimal:arm64. (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 ... 19611 files and directories currently installed.) Preparing to unpack .../libpython3.11-minimal_3.11.2-6_arm64.deb ... Unpacking libpython3.11-minimal:arm64 (3.11.2-6) ... Selecting previously unselected package libexpat1:arm64. Preparing to unpack .../libexpat1_2.5.0-1_arm64.deb ... Unpacking libexpat1:arm64 (2.5.0-1) ... Selecting previously unselected package python3.11-minimal. Preparing to unpack .../python3.11-minimal_3.11.2-6_arm64.deb ... Unpacking python3.11-minimal (3.11.2-6) ... Setting up libpython3.11-minimal:arm64 (3.11.2-6) ... Setting up libexpat1:arm64 (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 ... 19927 files and directories currently installed.) Preparing to unpack .../0-python3-minimal_3.11.2-1+b1_arm64.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:arm64. Preparing to unpack .../3-libreadline8_8.2-1.3_arm64.deb ... Unpacking libreadline8:arm64 (8.2-1.3) ... Selecting previously unselected package libpython3.11-stdlib:arm64. Preparing to unpack .../4-libpython3.11-stdlib_3.11.2-6_arm64.deb ... Unpacking libpython3.11-stdlib:arm64 (3.11.2-6) ... Selecting previously unselected package python3.11. Preparing to unpack .../5-python3.11_3.11.2-6_arm64.deb ... Unpacking python3.11 (3.11.2-6) ... Selecting previously unselected package libpython3-stdlib:arm64. Preparing to unpack .../6-libpython3-stdlib_3.11.2-1+b1_arm64.deb ... Unpacking libpython3-stdlib:arm64 (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 ... 20361 files and directories currently installed.) Preparing to unpack .../000-python3_3.11.2-1+b1_arm64.deb ... Unpacking python3 (3.11.2-1+b1) ... Selecting previously unselected package libproc2-0:arm64. Preparing to unpack .../001-libproc2-0_2%3a4.0.2-3_arm64.deb ... Unpacking libproc2-0:arm64 (2:4.0.2-3) ... Selecting previously unselected package procps. Preparing to unpack .../002-procps_2%3a4.0.2-3_arm64.deb ... Unpacking procps (2:4.0.2-3) ... Selecting previously unselected package sensible-utils. Preparing to unpack .../003-sensible-utils_0.0.17+nmu1_all.deb ... Unpacking sensible-utils (0.0.17+nmu1) ... Selecting previously unselected package libmagic-mgc. Preparing to unpack .../004-libmagic-mgc_1%3a5.44-3_arm64.deb ... Unpacking libmagic-mgc (1:5.44-3) ... Selecting previously unselected package libmagic1:arm64. Preparing to unpack .../005-libmagic1_1%3a5.44-3_arm64.deb ... Unpacking libmagic1:arm64 (1:5.44-3) ... Selecting previously unselected package file. Preparing to unpack .../006-file_1%3a5.44-3_arm64.deb ... Unpacking file (1:5.44-3) ... Selecting previously unselected package gettext-base. Preparing to unpack .../007-gettext-base_0.21-12_arm64.deb ... Unpacking gettext-base (0.21-12) ... Selecting previously unselected package libuchardet0:arm64. Preparing to unpack .../008-libuchardet0_0.0.7-1_arm64.deb ... Unpacking libuchardet0:arm64 (0.0.7-1) ... Selecting previously unselected package groff-base. Preparing to unpack .../009-groff-base_1.22.4-10_arm64.deb ... Unpacking groff-base (1.22.4-10) ... Selecting previously unselected package bsdextrautils. Preparing to unpack .../010-bsdextrautils_2.38.1-5+b1_arm64.deb ... Unpacking bsdextrautils (2.38.1-5+b1) ... Selecting previously unselected package libpipeline1:arm64. Preparing to unpack .../011-libpipeline1_1.5.7-1_arm64.deb ... Unpacking libpipeline1:arm64 (1.5.7-1) ... Selecting previously unselected package man-db. Preparing to unpack .../012-man-db_2.11.2-2_arm64.deb ... Unpacking man-db (2.11.2-2) ... Selecting previously unselected package libbsd0:arm64. Preparing to unpack .../013-libbsd0_0.11.7-2_arm64.deb ... Unpacking libbsd0:arm64 (0.11.7-2) ... Selecting previously unselected package libedit2:arm64. Preparing to unpack .../014-libedit2_3.1-20221030-2_arm64.deb ... Unpacking libedit2:arm64 (3.1-20221030-2) ... Selecting previously unselected package libcbor0.8:arm64. Preparing to unpack .../015-libcbor0.8_0.8.0-2+b1_arm64.deb ... Unpacking libcbor0.8:arm64 (0.8.0-2+b1) ... Selecting previously unselected package libfido2-1:arm64. Preparing to unpack .../016-libfido2-1_1.12.0-2+b1_arm64.deb ... Unpacking libfido2-1:arm64 (1.12.0-2+b1) ... Selecting previously unselected package openssh-client. Preparing to unpack .../017-openssh-client_1%3a9.2p1-2_arm64.deb ... Unpacking openssh-client (1:9.2p1-2) ... Selecting previously unselected package m4. Preparing to unpack .../018-m4_1.4.19-3_arm64.deb ... Unpacking m4 (1.4.19-3) ... Selecting previously unselected package autoconf. Preparing to unpack .../019-autoconf_2.71-3_all.deb ... Unpacking autoconf (2.71-3) ... Selecting previously unselected package autotools-dev. Preparing to unpack .../020-autotools-dev_20220109.1_all.deb ... Unpacking autotools-dev (20220109.1) ... Selecting previously unselected package automake. Preparing to unpack .../021-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 .../022-autopoint_0.21-12_all.deb ... Unpacking autopoint (0.21-12) ... Selecting previously unselected package libtcl8.6:arm64. Preparing to unpack .../023-libtcl8.6_8.6.13+dfsg-2_arm64.deb ... Unpacking libtcl8.6:arm64 (8.6.13+dfsg-2) ... Selecting previously unselected package libbrotli1:arm64. Preparing to unpack .../024-libbrotli1_1.0.9-2+b6_arm64.deb ... Unpacking libbrotli1:arm64 (1.0.9-2+b6) ... Selecting previously unselected package libpng16-16:arm64. Preparing to unpack .../025-libpng16-16_1.6.39-2_arm64.deb ... Unpacking libpng16-16:arm64 (1.6.39-2) ... Selecting previously unselected package libfreetype6:arm64. Preparing to unpack .../026-libfreetype6_2.12.1+dfsg-5_arm64.deb ... Unpacking libfreetype6:arm64 (2.12.1+dfsg-5) ... Selecting previously unselected package fonts-dejavu-core. Preparing to unpack .../027-fonts-dejavu-core_2.37-6_all.deb ... Unpacking fonts-dejavu-core (2.37-6) ... Selecting previously unselected package fontconfig-config. Preparing to unpack .../028-fontconfig-config_2.14.1-4_arm64.deb ... Unpacking fontconfig-config (2.14.1-4) ... Selecting previously unselected package libfontconfig1:arm64. Preparing to unpack .../029-libfontconfig1_2.14.1-4_arm64.deb ... Unpacking libfontconfig1:arm64 (2.14.1-4) ... Selecting previously unselected package libxau6:arm64. Preparing to unpack .../030-libxau6_1%3a1.0.9-1_arm64.deb ... Unpacking libxau6:arm64 (1:1.0.9-1) ... Selecting previously unselected package libxdmcp6:arm64. Preparing to unpack .../031-libxdmcp6_1%3a1.1.2-3_arm64.deb ... Unpacking libxdmcp6:arm64 (1:1.1.2-3) ... Selecting previously unselected package libxcb1:arm64. Preparing to unpack .../032-libxcb1_1.15-1_arm64.deb ... Unpacking libxcb1:arm64 (1.15-1) ... Selecting previously unselected package libx11-data. Preparing to unpack .../033-libx11-data_2%3a1.8.4-2_all.deb ... Unpacking libx11-data (2:1.8.4-2) ... Selecting previously unselected package libx11-6:arm64. Preparing to unpack .../034-libx11-6_2%3a1.8.4-2_arm64.deb ... Unpacking libx11-6:arm64 (2:1.8.4-2) ... Selecting previously unselected package libxrender1:arm64. Preparing to unpack .../035-libxrender1_1%3a0.9.10-1.1_arm64.deb ... Unpacking libxrender1:arm64 (1:0.9.10-1.1) ... Selecting previously unselected package libxft2:arm64. Preparing to unpack .../036-libxft2_2.3.6-1_arm64.deb ... Unpacking libxft2:arm64 (2.3.6-1) ... Selecting previously unselected package libxext6:arm64. Preparing to unpack .../037-libxext6_2%3a1.3.4-1+b1_arm64.deb ... Unpacking libxext6:arm64 (2:1.3.4-1+b1) ... Selecting previously unselected package x11-common. Preparing to unpack .../038-x11-common_1%3a7.7+23_all.deb ... Unpacking x11-common (1:7.7+23) ... Selecting previously unselected package libxss1:arm64. Preparing to unpack .../039-libxss1_1%3a1.2.3-1_arm64.deb ... Unpacking libxss1:arm64 (1:1.2.3-1) ... Selecting previously unselected package libtk8.6:arm64. Preparing to unpack .../040-libtk8.6_8.6.13-2_arm64.deb ... Unpacking libtk8.6:arm64 (8.6.13-2) ... Selecting previously unselected package tk8.6-blt2.5. Preparing to unpack .../041-tk8.6-blt2.5_2.5.3+dfsg-4.1_arm64.deb ... Unpacking tk8.6-blt2.5 (2.5.3+dfsg-4.1) ... Selecting previously unselected package blt. Preparing to unpack .../042-blt_2.5.3+dfsg-4.1_arm64.deb ... Unpacking blt (2.5.3+dfsg-4.1) ... Selecting previously unselected package clustalw. Preparing to unpack .../043-clustalw_2.1+lgpl-7_arm64.deb ... Unpacking clustalw (2.1+lgpl-7) ... Selecting previously unselected package libicu72:arm64. Preparing to unpack .../044-libicu72_72.1-3_arm64.deb ... Unpacking libicu72:arm64 (72.1-3) ... Selecting previously unselected package libxml2:arm64. Preparing to unpack .../045-libxml2_2.9.14+dfsg-1.2_arm64.deb ... Unpacking libxml2:arm64 (2.9.14+dfsg-1.2) ... Selecting previously unselected package libarchive13:arm64. Preparing to unpack .../046-libarchive13_3.6.2-1_arm64.deb ... Unpacking libarchive13:arm64 (3.6.2-1) ... Selecting previously unselected package libsasl2-modules-db:arm64. Preparing to unpack .../047-libsasl2-modules-db_2.1.28+dfsg-10_arm64.deb ... Unpacking libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Selecting previously unselected package libsasl2-2:arm64. Preparing to unpack .../048-libsasl2-2_2.1.28+dfsg-10_arm64.deb ... Unpacking libsasl2-2:arm64 (2.1.28+dfsg-10) ... Selecting previously unselected package libldap-2.5-0:arm64. Preparing to unpack .../049-libldap-2.5-0_2.5.13+dfsg-5_arm64.deb ... Unpacking libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Selecting previously unselected package libnghttp2-14:arm64. Preparing to unpack .../050-libnghttp2-14_1.52.0-1_arm64.deb ... Unpacking libnghttp2-14:arm64 (1.52.0-1) ... Selecting previously unselected package libpsl5:arm64. Preparing to unpack .../051-libpsl5_0.21.2-1_arm64.deb ... Unpacking libpsl5:arm64 (0.21.2-1) ... Selecting previously unselected package librtmp1:arm64. Preparing to unpack .../052-librtmp1_2.4+20151223.gitfa8646d.1-2+b2_arm64.deb ... Unpacking librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Selecting previously unselected package libssh2-1:arm64. Preparing to unpack .../053-libssh2-1_1.10.0-3+b1_arm64.deb ... Unpacking libssh2-1:arm64 (1.10.0-3+b1) ... Selecting previously unselected package libcurl4:arm64. Preparing to unpack .../054-libcurl4_7.88.1-10_arm64.deb ... Unpacking libcurl4:arm64 (7.88.1-10) ... Selecting previously unselected package libjsoncpp25:arm64. Preparing to unpack .../055-libjsoncpp25_1.9.5-4_arm64.deb ... Unpacking libjsoncpp25:arm64 (1.9.5-4) ... Selecting previously unselected package librhash0:arm64. Preparing to unpack .../056-librhash0_1.4.3-3_arm64.deb ... Unpacking librhash0:arm64 (1.4.3-3) ... Selecting previously unselected package libuv1:arm64. Preparing to unpack .../057-libuv1_1.44.2-1_arm64.deb ... Unpacking libuv1:arm64 (1.44.2-1) ... Selecting previously unselected package cmake-data. Preparing to unpack .../058-cmake-data_3.25.1-1_all.deb ... Unpacking cmake-data (3.25.1-1) ... Selecting previously unselected package cmake. Preparing to unpack .../059-cmake_3.25.1-1_arm64.deb ... Unpacking cmake (3.25.1-1) ... Selecting previously unselected package libdebhelper-perl. Preparing to unpack .../060-libdebhelper-perl_13.11.4_all.deb ... Unpacking libdebhelper-perl (13.11.4) ... Selecting previously unselected package libtool. Preparing to unpack .../061-libtool_2.4.7-5_all.deb ... Unpacking libtool (2.4.7-5) ... Selecting previously unselected package dh-autoreconf. Preparing to unpack .../062-dh-autoreconf_20_all.deb ... Unpacking dh-autoreconf (20) ... 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Setting up bsdextrautils (2.38.1-5+b1) ... Setting up libopenmm7.7 (7.7.0+dfsg-9+b1) ... Setting up libmagic-mgc (1:5.44-3) ... Setting up libarchive-zip-perl (1.68-1) ... Setting up libglib2.0-0:arm64 (2.74.6-2) ... No schema files found: doing nothing. Setting up libglvnd0:arm64 (1.6.0-1) ... Setting up libboost-program-options1.74.0:arm64 (1.74.0+ds1-21) ... Setting up fonts-lyx (2.3.7-1) ... Setting up voronota (1.22.3149-2) ... Setting up libcbor0.8:arm64 (0.8.0-2+b1) ... Setting up libdebhelper-perl (13.11.4) ... Setting up libbrotli1:arm64 (1.0.9-2+b6) ... Setting up libboost-chrono1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up x11-common (1:7.7+23) ... invoke-rc.d: could not determine current runlevel Setting up X socket directories... /tmp/.X11-unix /tmp/.ICE-unix. Setting up libsensors-config (1:3.6.0-7.1) ... Setting up libboost-stacktrace1.74.0:arm64 (1.74.0+ds1-21) ... Setting up libnghttp2-14:arm64 (1.52.0-1) ... Setting up libmagic1:arm64 (1:5.44-3) ... Setting up libdeflate0:arm64 (1.14-1) ... Setting up libfftw3-long3:arm64 (3.3.10-1) ... Setting up gettext-base (0.21-12) ... Setting up m4 (1.4.19-3) ... Setting up libboost-nowide1.74.0 (1.74.0+ds1-21) ... Setting up libqhull-r8.0:arm64 (2020.2-5) ... Setting up xkb-data (2.35.1-1) ... Setting up libboost-filesystem1.74.0:arm64 (1.74.0+ds1-21) ... Setting up libboost-exception1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up file (1:5.44-3) ... Setting up libboost-exception-dev:arm64 (1.74.0.3) ... Setting up sip-dev (4.19.25+dfsg-5+b1) ... Setting up libpthread-stubs0-dev:arm64 (0.4-1) ... Setting up libjbig0:arm64 (2.1-6.1) ... Setting up libopenmm-dev (7.7.0+dfsg-9+b1) ... Setting up libpcre2-16-0:arm64 (10.42-1) ... Setting up libopengl0:arm64 (1.6.0-1) ... Setting up libboost-program-options1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libsasl2-modules-db:arm64 (2.1.28+dfsg-10) ... Setting up unicode-data (15.0.0-1) ... Setting up libxsimd-dev:arm64 (8.1.0-7) ... Setting up xtrans-dev (1.4.0-1) ... Setting up autotools-dev (20220109.1) ... Setting up libz3-4:arm64 (4.8.12-3.1) ... Setting up libblas3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/blas/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode Setting up libpkgconf3:arm64 (1.8.1-1) ... Setting up libuv1:arm64 (1.44.2-1) ... Setting up libmunge2 (0.5.15-2) ... Setting up libexpat1-dev:arm64 (2.5.0-1) ... Setting up libboost-test1.74.0:arm64 (1.74.0+ds1-21) ... Setting up libjpeg62-turbo:arm64 (1:2.1.5-2) ... Setting up qt5-qmake-bin (5.15.8+dfsg-11) ... Setting up libsqlite3-dev:arm64 (3.40.1-2) ... Setting up libboost-program-options-dev:arm64 (1.74.0.3) ... Setting up libx11-data (2:1.8.4-2) ... Setting up libjpeg62-turbo-dev:arm64 (1:2.1.5-2) ... Setting up librtmp1:arm64 (2.4+20151223.gitfa8646d.1-2+b2) ... Setting up libavahi-common-data:arm64 (0.8-10) ... Setting up libboost-system1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libdbus-1-3:arm64 (1.14.6-1) ... Setting up libboost-nowide1.74-dev (1.74.0+ds1-21) ... Setting up libfribidi0:arm64 (1.0.8-2.1) ... Setting up libboost-regex1.74.0:arm64 (1.74.0+ds1-21) ... Setting up libimagequant0:arm64 (2.17.0-1) ... Setting up libproc2-0:arm64 (2:4.0.2-3) ... Setting up libpng16-16:arm64 (1.6.39-2) ... Setting up libhwloc15:arm64 (2.9.0-1) ... Setting up libevent-core-2.1-7:arm64 (2.1.12-stable-8) ... Setting up libboost-context1.74.0:arm64 (1.74.0+ds1-21) ... Setting up libevent-2.1-7:arm64 (2.1.12-stable-8) ... Setting up libboost-graph1.74.0:arm64 (1.74.0+ds1-21) ... Setting up libtcl8.6:arm64 (8.6.13+dfsg-2) ... Setting up libboost-random1.74.0:arm64 (1.74.0+ds1-21) ... Setting up autopoint (0.21-12) ... Setting up libjsoncpp25:arm64 (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:arm64 (1:3.6.0-7.1) ... Setting up liblerc-dev:arm64 (4.0.0+ds-2) ... Setting up libltdl7:arm64 (2.4.7-5) ... Setting up libfftw3-double3:arm64 (3.3.10-1) ... Setting up libcifpp-data (5.0.7.1-1) ... Setting up libglapi-mesa:arm64 (22.3.6-1+deb12u1) ... Setting up libsasl2-2:arm64 (2.1.28+dfsg-10) ... Setting up libgfortran5:arm64 (12.2.0-14) ... Setting up libmtdev1:arm64 (1.1.6-1) ... Setting up libvulkan1:arm64 (1.3.239.0-1) ... Setting up autoconf (2.71-3) ... Setting up libwebp7:arm64 (1.2.4-0.2) ... Setting up libboost-atomic1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libboost-math1.74.0:arm64 (1.74.0+ds1-21) ... Setting up liblzma-dev:arm64 (5.4.1-0.2) ... Setting up libboost-serialization1.74.0:arm64 (1.74.0+ds1-21) ... Setting up zlib1g-dev:arm64 (1:1.2.13.dfsg-1) ... Setting up libboost-atomic-dev:arm64 (1.74.0.3) ... Setting up libnuma1:arm64 (2.0.16-1) ... Setting up libboost-container1.74.0:arm64 (1.74.0+ds1-21) ... Setting up sensible-utils (0.0.17+nmu1) ... Setting up ocl-icd-libopencl1:arm64 (2.3.1-1) ... Setting up libxshmfence1:arm64 (1.3-1) ... Setting up librhash0:arm64 (1.4.3-3) ... Setting up libtiff6:arm64 (4.5.0-6) ... Setting up libuchardet0:arm64 (0.0.7-1) ... Setting up procps (2:4.0.2-3) ... Setting up libnl-3-200:arm64 (3.7.0-0.2+b1) ... Setting up openmpi-common (4.1.4-3) ... Setting up clustalw (2.1+lgpl-7) ... Setting up libmd4c0:arm64 (0.4.8-1) ... Setting up libopenjp2-7:arm64 (2.5.0-2) ... Setting up libsub-override-perl (0.09-4) ... Setting up libssh2-1:arm64 (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:arm64 (1.74.0.3) ... Setting up libglu1-mesa:arm64 (9.0.2-1.1) ... Setting up libboost-math1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libboost-filesystem1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libopengl-dev:arm64 (1.6.0-1) ... Setting up libjs-jquery (3.6.1+dfsg+~3.5.14-1) ... Setting up libboost-date-time1.74.0:arm64 (1.74.0+ds1-21) ... Setting up libfido2-1:arm64 (1.12.0-2+b1) ... Setting up libboost-python1.74.0 (1.74.0+ds1-21) ... Setting up libboost-fiber1.74.0:arm64 (1.74.0+ds1-21) ... Setting up libboost-stacktrace1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libboost-test1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up python-matplotlib-data (3.6.3-1) ... Setting up libwebpmux3:arm64 (1.2.4-0.2) ... Setting up libbsd0:arm64 (0.11.7-2) ... Setting up libtiffxx6:arm64 (4.5.0-6) ... Setting up libdeflate-dev:arm64 (1.14-1) ... Setting up libdrm-common (2.4.114-1) ... Setting up libelf1:arm64 (0.188-2.1) ... Setting up libevdev2:arm64 (1.13.0+dfsg-1) ... Setting up readline-common (8.2-1.3) ... Setting up libboost-timer1.74.0:arm64 (1.74.0+ds1-21) ... Setting up libicu-dev:arm64 (72.1-3) ... Setting up libxml2:arm64 (2.9.14+dfsg-1.2) ... Setting up libboost-filesystem-dev:arm64 (1.74.0.3) ... Setting up libgudev-1.0-0:arm64 (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:arm64 (1.74.0+ds1-21) ... Setting up libboost-numpy1.74.0 (1.74.0+ds1-21) ... Setting up libevent-pthreads-2.1-7:arm64 (2.1.12-stable-8) ... Setting up libwacom-common (2.6.0-1) ... Setting up libxkbcommon0:arm64 (1.5.0-1) ... Setting up libwayland-client0:arm64 (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:arm64 (2:1.0.10-1) ... Setting up libboost-log1.74.0 (1.74.0+ds1-21) ... Setting up libxdmcp6:arm64 (1:1.1.2-3) ... Setting up libevent-extra-2.1-7:arm64 (2.1.12-stable-8) ... Setting up liblapack3:arm64 (3.11.0-2) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/lapack/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode Setting up libxcb1:arm64 (1.15-1) ... Setting up gettext (0.21-12) ... Setting up libopenblas0-pthread:arm64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3 to provide /usr/lib/aarch64-linux-gnu/libblas.so.3 (libblas.so.3-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/liblapack.so.3 to provide /usr/lib/aarch64-linux-gnu/liblapack.so.3 (liblapack.so.3-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblas.so.0 to provide /usr/lib/aarch64-linux-gnu/libopenblas.so.0 (libopenblas.so.0-aarch64-linux-gnu) in auto mode Setting up libxcb-xfixes0:arm64 (1.15-1) ... Setting up libxau-dev:arm64 (1:1.0.9-1) ... Setting up qt5-qmake:arm64 (5.15.8+dfsg-11) ... Setting up libxcb-xinput0:arm64 (1.15-1) ... Setting up libtool (2.4.7-5) ... Setting up libboost-container1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libarchive13:arm64 (3.6.2-1) ... Setting up libxcb-render0:arm64 (1.15-1) ... Setting up libboost-chrono-dev:arm64 (1.74.0.3) ... Setting up libfftw3-bin (3.3.10-1) ... Setting up libwacom9:arm64 (2.6.0-1) ... Setting up fontconfig-config (2.14.1-4) ... Setting up libboost-math-dev:arm64 (1.74.0.3) ... Setting up libxcb-glx0:arm64 (1.15-1) ... Setting up libboost-coroutine1.74.0:arm64 (1.74.0+ds1-21) ... Setting up libwebpdemux2:arm64 (1.2.4-0.2) ... Setting up libedit2:arm64 (3.1-20221030-2) ... Setting up libreadline8:arm64 (8.2-1.3) ... Setting up libboost-system-dev:arm64 (1.74.0.3) ... Setting up libpng-dev:arm64 (1.6.39-2) ... Setting up libxcb-keysyms1:arm64 (0.4.0-1+b2) ... Setting up libxcb-shape0:arm64 (1.15-1) ... Setting up libavahi-common3:arm64 (0.8-10) ... Setting up libjpeg-dev:arm64 (1:2.1.5-2) ... Setting up libjbig-dev:arm64 (2.1-6.1) ... Setting up libevent-openssl-2.1-7:arm64 (2.1.12-stable-8) ... Setting up libxcb-render-util0:arm64 (0.3.9-1+b1) ... Setting up libboost-tools-dev (1.74.0.3) ... Setting up libgfortran-12-dev:arm64 (12.2.0-14) ... Setting up libxcb-shm0:arm64 (1.15-1) ... Setting up libxcb-icccm4:arm64 (0.4.1-1.1) ... Setting up libboost-nowide-dev (1.74.0.3) ... Setting up libldap-2.5-0:arm64 (2.5.13+dfsg-5) ... Setting up libboost-container-dev:arm64 (1.74.0.3) ... Setting up libxcb-util1:arm64 (0.4.0-1+b1) ... Setting up pkgconf:arm64 (1.8.1-1) ... Setting up libinput-bin (1.22.1-1) ... Setting up libxcb-xkb1:arm64 (1.15-1) ... Setting up libxcb-image0:arm64 (0.4.0-2) ... Setting up intltool-debian (0.35.0+20060710.6) ... Setting up libnuma-dev:arm64 (2.0.16-1) ... Setting up libnl-route-3-200:arm64 (3.7.0-0.2+b1) ... Setting up libboost-test-dev:arm64 (1.74.0.3) ... Setting up libxcb-present0:arm64 (1.15-1) ... Setting up libcifpp5:arm64 (5.0.7.1-1) ... Setting up dh-autoreconf (20) ... Setting up libltdl-dev:arm64 (2.4.7-5) ... Setting up libxdmcp-dev:arm64 (1:1.1.2-3) ... Setting up gfortran-12 (12.2.0-14) ... Setting up libwebp-dev:arm64 (1.2.4-0.2) ... Setting up libxcb-xinerama0:arm64 (1.15-1) ... Setting up libjs-jquery-ui (1.13.2+dfsg-1) ... Setting up libfreetype6:arm64 (2.12.1+dfsg-5) ... Setting up libtiff-dev:arm64 (4.5.0-6) ... Setting up libxcb-sync1:arm64 (1.15-1) ... Setting up shared-mime-info (2.2-1) ... Setting up libxkbcommon-x11-0:arm64 (1.5.0-1) ... Setting up libevent-dev (2.1.12-stable-8) ... Setting up libboost-random1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libeigen3-dev (3.4.0-4) ... Setting up libboost-timer1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libboost-numpy1.74-dev (1.74.0+ds1-21) ... Setting up pkg-config:arm64 (1.8.1-1) ... Setting up libqt5core5a:arm64 (5.15.8+dfsg-11) ... Setting up libjs-sphinxdoc (5.3.0-4) ... Setting up libboost-serialization1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libopenmm-plugins (7.7.0+dfsg-9+b1) ... Setting up libxcb-dri2-0:arm64 (1.15-1) ... Setting up dh-strip-nondeterminism (1.13.1-1) ... Setting up libboost-wave1.74.0:arm64 (1.74.0+ds1-21) ... Setting up libdrm2:arm64 (2.4.114-1+b1) ... Setting up dwz (0.15-1) ... Setting up libboost-regex1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libnl-3-dev:arm64 (3.7.0-0.2+b1) ... Setting up libopenblas0:arm64 (0.3.21+ds-4) ... Setting up groff-base (1.22.4-10) ... Setting up libqt5dbus5:arm64 (5.15.8+dfsg-11) ... Setting up libxcb-randr0:arm64 (1.15-1) ... Setting up libboost-stacktrace-dev:arm64 (1.74.0.3) ... Setting up libllvm15:arm64 (1:15.0.6-4+b1) ... Setting up libxslt1.1:arm64 (1.1.35-1) ... Setting up libcurl4:arm64 (7.88.1-10) ... Setting up libx11-6:arm64 (2:1.8.4-2) ... Setting up libharfbuzz0b:arm64 (6.0.0+dfsg-3) ... Setting up libhwloc-dev:arm64 (2.9.0-1) ... Setting up libfontconfig1:arm64 (2.14.1-4) ... Setting up libboost-locale1.74.0:arm64 (1.74.0+ds1-21) ... Setting up libqt5test5:arm64 (5.15.8+dfsg-11) ... Setting up libboost-regex-dev:arm64 (1.74.0.3) ... Setting up libsm6:arm64 (2:1.2.3-1) ... Setting up libfftw3-dev:arm64 (3.3.10-1) ... Setting up libqt5concurrent5:arm64 (5.15.8+dfsg-11) ... Setting up libavahi-client3:arm64 (0.8-10) ... Setting up libboost-timer-dev:arm64 (1.74.0.3) ... Setting up libboost-type-erasure1.74.0:arm64 (1.74.0+ds1-21) ... Setting up liblbfgsb0:arm64 (3.0+dfsg.4-1) ... Setting up libdrm-amdgpu1:arm64 (2.4.114-1+b1) ... Setting up libopenblas-pthread-dev:arm64 (0.3.21+ds-4) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so to provide /usr/lib/aarch64-linux-gnu/libblas.so (libblas.so-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/liblapack.so to provide /usr/lib/aarch64-linux-gnu/liblapack.so (liblapack.so-aarch64-linux-gnu) in auto mode update-alternatives: using /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblas.so to provide /usr/lib/aarch64-linux-gnu/libopenblas.so (libopenblas.so-aarch64-linux-gnu) in auto mode Setting up libxcb-dri3-0:arm64 (1.15-1) ... Setting up libinput10:arm64 (1.22.1-1) ... Setting up libx11-xcb1:arm64 (2:1.8.4-2) ... Setting up libibverbs1:arm64 (44.0-2) ... Setting up fontconfig (2.14.1-4) ... Regenerating fonts cache... done. Setting up libdrm-nouveau2:arm64 (2.4.114-1+b1) ... Setting up libxcb1-dev:arm64 (1.15-1) ... Setting up libboost-wave1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libxrender1:arm64 (1:0.9.10-1.1) ... Setting up libgbm1:arm64 (22.3.6-1+deb12u1) ... Setting up ibverbs-providers:arm64 (44.0-2) ... Setting up libdrm-radeon1:arm64 (2.4.114-1+b1) ... Setting up openssh-client (1:9.2p1-2) ... Setting up po-debconf (1.0.21+nmu1) ... Setting up libpython3.11-stdlib:arm64 (3.11.2-6) ... Setting up libgl1-mesa-dri:arm64 (22.3.6-1+deb12u1) ... Setting up libx11-dev:arm64 (2:1.8.4-2) ... Setting up libxext6:arm64 (2:1.3.4-1+b1) ... Setting up libboost-random-dev:arm64 (1.74.0.3) ... Setting up libboost-wave-dev:arm64 (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:arm64 (5.15.8+dfsg-11) ... Setting up libxxf86vm1:arm64 (1:1.1.4-1+b2) ... Setting up libxnvctrl0:arm64 (525.85.05-1) ... Setting up libqt5sql5:arm64 (5.15.8+dfsg-11) ... Setting up libboost-iostreams1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libnl-route-3-dev:arm64 (3.7.0-0.2+b1) ... Setting up libboost-date-time1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up qtbase5-dev-tools (5.15.8+dfsg-11) ... Setting up libopenblas-dev:arm64 (0.3.21+ds-4) ... Setting up libqt5xml5:arm64 (5.15.8+dfsg-11) ... Setting up libegl-mesa0:arm64 (22.3.6-1+deb12u1) ... Setting up libxfixes3:arm64 (1:6.0.0-2) ... Setting up libboost-graph1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libraqm0:arm64 (0.7.0-4.1) ... Setting up libboost-numpy-dev (1.74.0.3) ... Setting up libboost-serialization-dev:arm64 (1.74.0.3) ... Setting up libboost-date-time-dev:arm64 (1.74.0.3) ... Setting up libxext-dev:arm64 (2:1.3.4-1+b1) ... Setting up libcups2:arm64 (2.4.2-3) ... Setting up libegl1:arm64 (1.6.0-1) ... Setting up cmake (3.25.1-1) ... Setting up libboost-thread1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libxss1:arm64 (1:1.2.3-1) ... Setting up libboost-thread-dev:arm64 (1.74.0.3) ... Setting up libpython3-stdlib:arm64 (3.11.2-1+b1) ... Setting up librdmacm1:arm64 (44.0-2) ... Setting up libboost-graph-dev:arm64 (1.74.0.3) ... Setting up python3.11 (3.11.2-6) ... Setting up libucx0:arm64 (1.13.1-1) ... Setting up libxft2:arm64 (2.3.6-1) ... Setting up libglx-mesa0:arm64 (22.3.6-1+deb12u1) ... Setting up libboost-log1.74-dev (1.74.0+ds1-21) ... Setting up libpython3.11:arm64 (3.11.2-6) ... Setting up libglx0:arm64 (1.6.0-1) ... Setting up libtk8.6:arm64 (8.6.13-2) ... Setting up debhelper (13.11.4) ... Setting up python3 (3.11.2-1+b1) ... Setting up libboost-iostreams-dev:arm64 (1.74.0.3) ... Setting up libibverbs-dev:arm64 (44.0-2) ... Setting up libhwloc-plugins:arm64 (2.9.0-1) ... Setting up libboost-context1.74-dev:arm64 (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:arm64 (1.74.0+ds1-21) ... Setting up python3-decorator (5.1.1-3) ... Setting up python3-packaging (23.0-1) ... Setting up libgl1:arm64 (1.6.0-1) ... Setting up libboost-type-erasure1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up python3-pyparsing (3.0.9-1) ... Setting up libpython3.11-dev:arm64 (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:arm64 (1.74.0+ds1-21) ... Setting up python3-pyqt5.sip (12.11.1-1) ... Setting up python3-lxml:arm64 (4.9.2-1+b1) ... Setting up libglx-dev:arm64 (1.6.0-1) ... Setting up python3-dateutil (2.8.2-2) ... Setting up libboost-coroutine1.74-dev:arm64 (1.74.0+ds1-21) ... Setting up libboost-coroutine-dev:arm64 (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:arm64 (1.6.0-1) ... Setting up libboost-fiber-dev:arm64 (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) ... Setting up libfabric1:arm64 (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:arm64 (1.3.239.0-1) ... Setting up libpython3-dev:arm64 (3.11.2-1+b1) ... Setting up libegl-dev:arm64 (1.6.0-1) ... Setting up libpmix2:arm64 (4.2.2-1+b1) ... Setting up python3-lz4 (4.0.2+dfsg-1+b2) ... Setting up python3.11-dev (3.11.2-6) ... Setting up libopenmpi3:arm64 (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:arm64 (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:arm64 (3.11.2-3) ... Setting up libboost-locale-dev:arm64 (1.74.0.3) ... Setting up libqt5widgets5:arm64 (5.15.8+dfsg-11) ... Setting up libboost-context-dev:arm64 (1.74.0.3) ... Setting up libqt5help5:arm64 (5.15.8-2) ... Setting up libboost-type-erasure-dev:arm64 (1.74.0.3) ... Setting up python3-fs (2.4.16-2) ... Setting up python3-beniget (0.4.1-3) ... Setting up libqt5printsupport5:arm64 (5.15.8+dfsg-11) ... Setting up libpython3-all-dev:arm64 (3.11.2-1+b1) ... Setting up python3-dev (3.11.2-1+b1) ... Setting up libglu1-mesa-dev:arm64 (9.0.2-1.1) ... Setting up python3-numpy (1:1.24.2-1) ... Setting up qtbase5-dev:arm64 (5.15.8+dfsg-11) ... Setting up libqt5opengl5:arm64 (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:arm64 (4.2.2-1+b1) ... 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:arm64 (5.15.8-2) ... Setting up libqt5opengl5-dev:arm64 (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:arm64 (4.1.4-3+b1) ... update-alternatives: using /usr/lib/aarch64-linux-gnu/openmpi/include to provide /usr/include/aarch64-linux-gnu/mpi (mpi-aarch64-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:arm64 (9.4.0-1.1+b1) ... Setting up python3-pil.imagetk:arm64 (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) ... 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/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 arm64 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/openstructure-2.3.1' dh_auto_configure -- -DOPTIMIZE=ON -DUBUNTU_LAYOUT=ON -DENABLE_MM=ON -DOPEN_MM_PLUGIN_DIR=/usr/lib/aarch64-linux-gnu/openmm/plugins cd obj-aarch64-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/aarch64-linux-gnu -DOPTIMIZE=ON -DUBUNTU_LAYOUT=ON -DENABLE_MM=ON -DOPEN_MM_PLUGIN_DIR=/usr/lib/aarch64-linux-gnu/openmm/plugins .. -- 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/aarch64-linux-gnu/libOpenGL.so -- Found EIGEN: /usr/include/eigen3 (Required is at least version "3.2.0") -- Found SQLITE3: /usr/lib/aarch64-linux-gnu/libsqlite3.so (Required is at least version "3.7.13") -- Found ZLIB: /usr/lib/aarch64-linux-gnu/libz.so (found version "1.2.13") -- Found PNG: /usr/lib/aarch64-linux-gnu/libpng.so (found version "1.6.39") -- Found FFTW: /usr/lib/aarch64-linux-gnu/libfftw3f.so -- Found TIFF: /usr/lib/aarch64-linux-gnu/libtiff.so (found version "4.5.0") -- Found OpenMM: /usr/lib/aarch64-linux-gnu/libOpenMM.so -- 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) : ON OpenMM plugins (-DOPEN_MM_PLUGIN_DIR) : /usr/lib/aarch64-linux-gnu/openmm/plugins 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/openstructure-2.3.1/obj-aarch64-linux-gnu make[1]: Leaving directory '/build/openstructure-2.3.1' dh_auto_build cd obj-aarch64-linux-gnu && make -j8 "INSTALL=install --strip-program=true" VERBOSE=1 make[1]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/openstructure-2.3.1 -B/build/openstructure-2.3.1/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/openstructure-2.3.1/obj-aarch64-linux-gnu/CMakeFiles /build/openstructure-2.3.1/obj-aarch64-linux-gnu//CMakeFiles/progress.marks make -f CMakeFiles/Makefile2 all make[2]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src/CMakeFiles/create_stage.dir/DependInfo.cmake --color= make -f modules/base/pymod/CMakeFiles/subst___init__.py.dir/build.make modules/base/pymod/CMakeFiles/subst___init__.py.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod/CMakeFiles/subst___init__.py.dir/DependInfo.cmake --color= make -f modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build.make modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/DependInfo.cmake --color= 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/pymod/CMakeFiles/ost_conop_pymod.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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/pymod/CMakeFiles/ost_db_pymod.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 -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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod/CMakeFiles/ost_geom_pymod.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/pymod/CMakeFiles/ost_gfx_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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/share /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share/CMakeFiles/scene_icons.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build.make modules/db/pymod/CMakeFiles/ost_db_pymod.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/pymod/./__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/db/./__init__.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build.make modules/gfx/pymod/CMakeFiles/ost_gfx_pymod.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib make -f modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build.make modules/bindings/pymod/CMakeFiles/ost_bindings_pymod.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/pymod/./__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./__init__.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./__init__.py make -f modules/base/pymod/CMakeFiles/subst___init__.py.dir/build.make modules/base/pymod/CMakeFiles/subst___init__.py.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -DINPUT_FILE=/build/openstructure-2.3.1/modules/base/pymod/__init__.py.in -DOUT_FILE=__init__.py -DALL_ADDITIONAL_MODULES=,\'gui\',\'gfx\',\'img\',\'info\' -P /build/openstructure-2.3.1/cmake_support/substitute.cmake make -f modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build.make modules/conop/pymod/CMakeFiles/ost_conop_pymod.dir/build make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/pymod/./__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./__init__.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/pymod/./__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/geom/./__init__.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/gui/share/CMakeFiles/scene_icons.dir/build.make modules/gui/share/CMakeFiles/scene_icons.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/bin cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./lga.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./lga.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/add_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/add_icon.png cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/pymod/./py_gfx_obj.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./py_gfx_obj.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 0%] Built target ost_db_pymod cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/pymod/./cleanup.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./cleanup.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/share /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share/CMakeFiles/gui_images.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/openstructure/libexec [ 0%] Built target subst___init__.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/gui/share/CMakeFiles/gui_images.dir/build.make modules/gui/share/CMakeFiles/gui_images.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/images/logo-small.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/images/logo-small.png make -f modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./hbplus.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hbplus.py [ 0%] Built target ost_geom_pymod make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_scene_pymod.dir/DependInfo.cmake --color= 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]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_dng_pymod.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-aarch64-linux-gnu/tests make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/close_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/close_icon.png [ 0%] Built target ost_gfx_pymod make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/__init__.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./msms.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./msms.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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 [ 0%] Built target gui_images make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/__init__.py [ 0%] Built target ost_conop_pymod 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/pymod/CMakeFiles/ost_img_pymod.dir/DependInfo.cmake --color= 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 cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/critical_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/critical_icon.png make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/pymod/CMakeFiles/ost_img_alg_pymod.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./tmtools.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./tmtools.py [ 0%] Built target create_stage make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build.make modules/gui/pymod/CMakeFiles/ost_gui_pymod.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/delete_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/delete_icon.png cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/color_options_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_options_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./__init__.py 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/pymod/CMakeFiles/ost_info_pymod.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/distance_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/distance_icon.png cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./dssp.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dssp.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/pymod/./__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/alg/./__init__.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/termuse.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/termuse.py 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/pymod/./__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/./__init__.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/superpositiondialog.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/superpositiondialog.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/color_select_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_select_widget.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/init.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/init.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/dng/menu.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/menu.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./init_context_menu.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_context_menu.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build.make modules/info/pymod/CMakeFiles/ost_info_pymod.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./clustalw.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./clustalw.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/pymod/./__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/info/./__init__.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/find_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/find_icon.png cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/combo_options_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/combo_options_widget.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./init_menubar.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_menubar.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/information_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/information_icon.png [ 0%] Built target ost_gui_dng_pymod 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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/pymod/CMakeFiles/ost_io_pymod.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/cpk_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/cpk_widget.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/map_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/map_icon.png make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/menubar_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/menubar_icon.png cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./utils.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./utils.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/custom_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/custom_widget.py [ 0%] Built target ost_info_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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/pymod/CMakeFiles/ost_mol_pymod.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/rigid_body_manipulator_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/rigid_body_manipulator_icon.png make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build.make modules/io/pymod/CMakeFiles/ost_io_pymod.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./init_spacenav.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_spacenav.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/pymod/./__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./__init__.py [ 0%] Built target ost_img_pymod 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/ost_mol_alg_pymod.dir/DependInfo.cmake --color= [ 0%] Built target ost_img_alg_pymod cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/selection_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/selection_icon.png cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_editor_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_editor_widget.py make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./init_splash.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_splash.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/pymod/./__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/./__init__.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./naccess.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./naccess.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' 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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/pymod/./remote.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./remote.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./__init__.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_info_handler.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_info_handler.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/show_sidebar_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/show_sidebar_icon.png make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/pymod/./repository.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./repository.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./trajectory_viewer.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./trajectory_viewer.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_list_model.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_list_model.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./forcefield.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./forcefield.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./hhblits.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits.py [ 0%] Built target ost_mol_pymod make -f modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build.make modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/site_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/site_icon.png cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./views.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./views.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./helpwidget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./helpwidget.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_preset_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_preset_widget.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./ff_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./ff_reader.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build.make modules/mol/mm/pymod/CMakeFiles/ost_mol_mm_pymod.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./superpose.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./superpose.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./hhblits2.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits2.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/pymod/./__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./__init__.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./table.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./table.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./qsscoring.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./qsscoring.py [ 0%] Built target ost_io_pymod cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./buildingblock.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./buildingblock.hh 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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/split_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/split_icon.png make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/pymod/CMakeFiles/ost_seq_pymod.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./trajectory_analysis.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./trajectory_analysis.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/hsc_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/hsc_widget.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/pymod/./antechamber.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./antechamber.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./hhblits3.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits3.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/warning_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/warning_icon.png make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/pymod/./__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/./__init__.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/./gosty_startup.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./gosty_startup.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./block_modifiers.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./block_modifiers.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./structure_analysis.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./structure_analysis.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./blast.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./blast.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/immutable_gradient_info_handler.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_gradient_info_handler.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./helix_kinks.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./helix_kinks.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./cadscore.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./cadscore.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/immutable_preset_info_handler.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/immutable_preset_info_handler.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/share && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/share/icons/refresh.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/gui/icons/refresh.png make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./gromacs_block_modifiers.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./gromacs_block_modifiers.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 0%] Built target ost_seq_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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/pymod/./hbond.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./hbond.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/ost_seq_alg_pymod.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/init_inspector.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/init_inspector.py [ 0%] Built target ost_mol_mm_pymod cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./kclust.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./kclust.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./heuristic_block_modifiers.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./heuristic_block_modifiers.hh make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts/CMakeFiles/subst_ost_startup.py.dir/DependInfo.cmake --color= [ 0%] Built target ost_gui_pymod make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/inspector_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/inspector_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts/CMakeFiles/subst_ost_config.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' 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]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/./__init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./__init__.py [ 0%] Built target scene_icons cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./interaction.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./interaction.hh make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./ialign.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./ialign.py [ 0%] Built target ost_mol_alg_pymod make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts/CMakeFiles/subst_ost.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/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/openstructure-2.3.1/cmake_support/substitute.cmake make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts/CMakeFiles/subst_dng.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/map_level_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/map_level_widget.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/./mat.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./mat.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/pymod/./mmseqs2.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./mmseqs2.py make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/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/openstructure-2.3.1/cmake_support/substitute.cmake cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./settings.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./settings.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/./renumber.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./renumber.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/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/openstructure-2.3.1/cmake_support/substitute.cmake make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/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/openstructure-2.3.1/cmake_support/substitute.cmake [ 0%] Built target subst_ost_startup.py make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./simulation.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./simulation.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/actions /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/actions /build/openstructure-2.3.1/obj-aarch64-linux-gnu/actions/CMakeFiles/actions.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/./aaindex.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./aaindex.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/remote.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/remote.py [ 0%] Built target ost_bindings_pymod [ 0%] Built target subst_ost make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/depend make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom_headers.dir/DependInfo.cmake --color= make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./modeller.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./modeller.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/aaindex1 /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/aaindex/aaindex1 [ 0%] Built target subst_ost_config make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/config /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/config /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/config/CMakeFiles/ost_config_headers.dir/DependInfo.cmake --color= make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src/CMakeFiles/ost_base_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./observer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./observer.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_editor_list_model.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_list_model.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/export_helper/vector.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/export_helper/vector.hh make -f actions/CMakeFiles/actions.dir/build.make actions/CMakeFiles/actions.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/actions && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/actions/ost-compare-structures /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/openstructure/libexec/ost-compare-structures [ 0%] Built target subst_dng 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod/CMakeFiles/ost_base_pymod.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/build 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./base.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/generic_property_def.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/export_helper/generic_property_def.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_editor_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_widget.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/aaindex2 /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/aaindex/aaindex2 cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./def.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./def.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./config.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build.make modules/base/pymod/CMakeFiles/ost_base_pymod.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./state_extractor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./state_extractor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./exc.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./exc.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./settings.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./settings.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/pymod/aaindex3 /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/aaindex/aaindex3 cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/pair_to_tuple_conv.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_info_handler.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_info_handler.py [ 0%] Built target actions make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_list_model.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_list_model.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./stutil.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.py make -f modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/depend [ 0%] Built target ost_seq_alg_pymod make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src /build/openstructure-2.3.1/obj-aarch64-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]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src/CMakeFiles/ost_info_headers.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./geom.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./geom.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./system_creator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./system_creator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./dllexport.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./dllexport.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/vec_to_list_conv.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/export_helper/vec_to_list_conv.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/preset_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_widget.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./table.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./version.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./version.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/render_mode_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_mode_widget.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./table_selector.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table_selector.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/test_utils/compare_files.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/test_utils/compare_files.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./mat.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./generic_property.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./generic_property.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh [ 0%] Built target ost_config_headers 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]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./topology_creator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./topology_creator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/render_op.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_op.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat2.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./mat2.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./xmlrunner.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./integrity_error.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./integrity_error.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_error.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_error.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./index.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./index.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_iterator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat3.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./mat3.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/render_options_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_options_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/pointer_iterator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./invalid_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./invalid_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/pymod/./testutils.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./testutils.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./topology.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./topology.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat4.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./mat4.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/scene_observer_impl.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_observer_impl.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./steep.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./steep.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_list.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./sequence_list.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_group.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_group.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/cmake -E copy_if_different __init__.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/__init__.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/scene_selection_helper.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_selection_helper.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./ptr_observer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./ptr_observer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_prop.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_prop.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec2.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec2.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./sequence_handle.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./log.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./log.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/simple_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/simple_widget.py [ 0%] Built target ost_base_pymod [ 0%] Built target ost_mol_mm_headers make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_group.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_group.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec3.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec3.hh make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./alignment_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./alignment_handle.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./log_sink.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./log_sink.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/sline_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/sline_widget.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec4.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec4.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/src/./wrap_tmalign.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/bindings/./wrap_tmalign.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_item.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_item.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/toolbar_options_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/toolbar_options_widget.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./profile.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./profile.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./conop.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./conop.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./sequence_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vecmat_op.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./processor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./processor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./dyn_cast.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./dyn_cast.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat2_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_region.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./aligned_region.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./module_config.hh [ 0%] Built target ost_bindings_headers cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/trace_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/trace_widget.py 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src/CMakeFiles/ost_db_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./amino_acids.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./amino_acids.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./stdint.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./stdint.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat3_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_column.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./aligned_column.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/tube_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/tube_widget.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_path.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_path.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./diag.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./diag.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./stdint_msc.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./stdint_msc.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat4_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/uniform_color_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/uniform_color_widget.py make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./sqlite_wrap.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/db/./sqlite_wrap.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_set.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_set.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_column_iterator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./aligned_column_iterator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./range.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./range.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./circular_iterator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./circular_iterator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./sqlite_conv.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/db/./sqlite_conv.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./model_check.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./model_check.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/visibility_op.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/visibility_op.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/dihedral.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./invalid_sequence.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./invalid_sequence.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_visitor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_visitor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./constants.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./constants.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_verbose_visitor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_verbose_visitor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./heuristic.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./heuristic.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/db/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./item_type.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./item_type.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/line_trace_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/line_trace_widget.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./views_from_sequences.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./linear_indexer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/db/./linear_indexer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./compound.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./units.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./units.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./profile_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./profile_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./geom_info_conversion.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./geom_info_conversion.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/wireframe_widget.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/wireframe_widget.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite2.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite2.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./message.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./message.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./binary_container.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/db/./binary_container.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/fragment_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound_lib.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./compound_lib.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./item_type_cast.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./item_type_cast.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./platform.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./platform.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/query_editor.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/query_editor.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite3.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite3.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./extract_data_helper.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/db/./extract_data_helper.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/fragment_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./module_config.hh [ 0%] Built target ost_seq_headers 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./string_ref.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./string_ref.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./rule_based.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./rule_based.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/query_ast.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./alignment_opts.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./alignment_opts.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./clip_alignment.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./conservation.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./conservation.hh [ 0%] Built target ost_gui_scene_pymod cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./minimal_compound_lib.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh [ 0%] Built target ost_info_headers [ 0%] Built target ost_db_headers make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./pod_vector.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./pod_vector.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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite2_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite2_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./contact_prediction_score.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./contact_prediction_score.hh make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src/CMakeFiles/ost_io_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound_lib_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite3_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite3_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./fixed_string.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./fixed_string.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/query_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./ring_finder.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./ring_finder.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./aligned_cuboid.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./aligned_cuboid.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./contact_weight_matrix.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.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/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./anisotropic.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./anisotropic.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./tri_matrix.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./tri_matrix.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/query_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec_mat_predicates.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec_mat_predicates.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./auto_correlate.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/star_parser.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/star_parser.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./quat.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./quat.hh [ 0%] Built target ost_conop_headers 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 cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./clear.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./clear.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/dispatch.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/dispatch.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./distance_map.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./distance_map.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./boost_filesystem_helper.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./transform.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./transform.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/residue_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./clip_min_max.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./clip_min_max.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./svd_superpose.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./svd_superpose.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/surface_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./conjugate.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./conjugate.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./paged_array.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./paged_array.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./entropy.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./entropy.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./point_cloud.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./point_cloud.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/surface_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/io_profile.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/io_profile.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_base.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./convolute.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./convolute.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./global_align.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./global_align.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_base_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./sec_structure_segments.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh [ 0%] Built target ost_base_headers make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./ins_del.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./ins_del.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_def.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_factory.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./correlate.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./correlate.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./local_dist_diff_test.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./local_dist_diff_test.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_crd_handler.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_frequency_domain.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_frequency_domain.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./cross_correlate.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./cross_correlate.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./distance_test_common.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./distance_test_common.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./local_align.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./local_align.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 cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./distance_rmsd_test.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./distance_rmsd_test.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_pqr_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./merge_pairwise_alignments.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./merge_pairwise_alignments.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./density_slice.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./density_slice.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./dft.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./dft.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./atom_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./superpose_frames.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_mae_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fft.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fft.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_spec.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./atom_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_spatial_domain.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./filter_clashes.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_option_group.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./pair_subst_weight_matrix.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./pair_subst_weight_matrix.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fftw_helper.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fftw_helper.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_view.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./atom_view.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./semiglobal_align.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./semiglobal_align.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./construct_cbeta.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fill.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fill.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bond_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./bond_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_algorithm.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./clash_score.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./sequence_identity.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./sequence_identity.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./filter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./filter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_pdb_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bond_table.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./bond_table.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fourier_filters.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./trajectory_analysis.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./trajectory_analysis.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/custom_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./sequence_similarity.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./sequence_similarity.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian_gradient_magnitude.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./gaussian_gradient_magnitude.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./structure_analysis.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./structure_analysis.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_writer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_writer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./chain_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/index.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/index.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_option.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_option.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./subst_weight_matrix.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./subst_weight_matrix.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./chain_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_sdf_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./gaussian.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./variance_map.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/type_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/type_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./pdbize.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./pdbize.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/value_holder.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/value_holder.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/sdf_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/sdf_reader.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_view.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./chain_view.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian_laplacian.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./adjacency_bitmap.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./adjacency_bitmap.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./data/default_contact_weight_matrix.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./default_contact_weight_matrix.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./algorithm.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./algorithm.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_widget.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_options_widget.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_type.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./chain_type.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./highest_peak_search_3d.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./highest_peak_search_3d.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./data/default_pair_subst_weight_matrix.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./circle_mask.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./circle_mask.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/save_entity.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/save_entity.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/manipulator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chem_class.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./chem_class.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./histogram.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./histogram.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./hmm_pseudo_counts.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./contact_overlap.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./composite_mask.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./composite_mask.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/line_trace_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/load_entity.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/load_entity.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./domain_find.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./line_iterator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./line_iterator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./hmm_score.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chem_type.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./chem_type.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_algorithm.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./data_algorithm.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./local_sigma_threshold.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./local_sigma_threshold.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/surface_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./similarity_matrix.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./similarity_matrix.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_group.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./coord_group.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/map_tool.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_observer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./data_observer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/load_surface.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/load_surface.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./accessibility.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./accessibility.hh [ 0%] Built target ost_seq_alg_headers make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/config /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/config /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/config/CMakeFiles/ost_config.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/surface_io_msms_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./mask_image.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./mask_image.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_source.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./coord_source.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_types.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./data_types.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./sec_struct.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./sec_struct.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Nothing to be done for 'modules/config/CMakeFiles/ost_config.dir/build'. make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./nonstandard.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./nonstandard.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./in_mem_coord_source.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./in_mem_coord_source.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_row.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./negate.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./negate.hh [ 0%] Built target ost_config cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./data.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./molck.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./molck.hh make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_frame.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./coord_frame.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/background_painter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./find_membrane.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./find_membrane.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./normalizer_factory.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./normalizer_factory.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/omf.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/omf.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./debug.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./debug.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./editor_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./editor_base.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./entity_to_density.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/conservation_painter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./editor_type_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./norm.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./dllexport.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./dllexport.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat2.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/load_map.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/load_map.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/src/mat2.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/painter.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./mol.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./mol.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent_iterator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./extent_iterator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/secstr_row.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh [ 0%] Built target ost_mol_alg_headers cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./normalizer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./normalizer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/tabulated_trig.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/tabulated_trig.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent_mask.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./extent_mask.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/image_format.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/image_format.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat3.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_secstr_painter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/src/mat3.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_linear.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./norm_linear.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/fast_spheres.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_dx_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_selection_painter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./extent.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_text_painter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_log.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./norm_log.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_spi_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_factory.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image_factory.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_delegate.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_od.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./norm_od.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_model.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_observer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_observer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/line_render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_situs_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./power_spectrum.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./power_spectrum.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_row.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./randomize.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./randomize.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_search_bar.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_observer_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/custom_render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/custom_render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_handle_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image_handle_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_property_mapper.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./smooth_mask_image.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./smooth_mask_image.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/cpk_render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/cpk_render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_table_view.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_mrc_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_view.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_view.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./stat.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/simple_render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_dat_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_visitor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_visitor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat_accumulator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./stat_accumulator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/sline_render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/sline_render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_list.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image_list.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/tick_painter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_ipl_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_visitor_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat_min_max.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./stat_min_max.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/line_trace_render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_state_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image_state_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_jpk_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/title_row.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./handle_type_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./handle_type_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./threshold.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./threshold.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_nanoscope_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/cartoon_render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/cartoon_render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/alignment_view_object.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./ics_editor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./ics_editor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_state.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image_state.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_png_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transcendentals.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transcendentals.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_view_object.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./not_connected_error.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./not_connected_error.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/trace_render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_view_object.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transform.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transform.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./property_id.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./property_id.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./inverted_mask.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./inverted_mask.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/tiff_util.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./map.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./map.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transform_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transform_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/jpk_util.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/jpk_util.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/main_thread_runner.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./query.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/fasta_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_transform.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./alg_transform.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_base_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_base_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/completer_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/completer_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/dir_model.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_error.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./query_error.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/uniform_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_visitor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_visitor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_mirror.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./alg_mirror.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/profile_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/gutter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/gutter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./mask.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_shift.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./alg_shift.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_state.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./query_state.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/path_completer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/path_completer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./discrete_shrink.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./discrete_shrink.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/entity_view_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transformation_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_context_parser.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_context_parser.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/basic_gradient_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/hhm_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/hhm_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./residue_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transformations.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transformations.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_completer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_completer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./residue_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./normalizer_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./normalizer_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fractional_shift.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fractional_shift.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./normalizer_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./normalizer_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/pssm_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/pssm_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_shell.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_prop.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./residue_prop.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/map_handle_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_view.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./residue_view.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_widget.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./render_pass.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./render_pass.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./null_data.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./null_data.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./bitmap_io.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./polar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./polar.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/load.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/load.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./collada_exporter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./sec_structure.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./sec_structure.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/save.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/save.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./observable.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./observable.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./color.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./color.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./spatial_organizer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./spatial_organizer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./line_average.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./line_average.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_tokenizer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_tokenizer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./binary_data_sink.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./binary_data_sink.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_manager.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./io_manager.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./binary_data_source.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./binary_data_source.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./entity.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./entity.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./rscrosscorr.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./rscrosscorr.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./paste_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./paste_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./surface.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_syntax_highlighter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_syntax_highlighter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./entity_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./entity_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_builder.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./surface_builder.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gl_helper.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gl_helper.hh [ 0%] Built target ost_img_alg_headers cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./peak.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./peak.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./container_serialization.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./container_serialization.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./builder.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./builder.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./phase.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./phase.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./surface_handle.hh [ 0%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/mat4.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/src/mat4.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./physical_units.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./physical_units.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./swap_util.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./swap_util.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_prop.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./surface_prop.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./pixel_sampling.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./pixel_sampling.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_utils.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./io_utils.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_text_document_layout.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_text_document_layout.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_exception.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./io_exception.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./point_list.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./point_list.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./torsion_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./torsion_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node_visitor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./convert.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./convert.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./point.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./point.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/shell_history.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/shell_history.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./polygon_mask.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./polygon_mask.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_object_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./converting_streams.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./converting_streams.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/state_machine.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/state_machine.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./transfer_connectivity.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./transfer_connectivity.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/state.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/state.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_object.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./formatted_line.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./formatted_line.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./progress.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./progress.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/transition.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/transition.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/chemdict_parser.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./chemdict_parser.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_view_wrapper.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./query_view_wrapper.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./size.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./size.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/star_parser.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./star_parser.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/transition_guard.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_object_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./spherical_mask.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./spherical_mask.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/mmcif_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./mmcif_reader.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./util.cc /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./util.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./view_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/mmcif_info.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./mmcif_info.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./util.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./util.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_prim.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_prim.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/io_profile.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./io_profile.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/button_bar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/button_bar.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/dcd_io.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./dcd_io.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/drop_box.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_crd_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_crd_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_type_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./view_type_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./value_util.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./value_util.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./symmetry_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./symmetry_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./vecmat.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./vecmat.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_test_object.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_test_object.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/panel_bar.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_info_convert.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_info_convert.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_pqr_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./glwin_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./glwin_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_manager.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/panel_manager.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./view_op.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/bottom_bar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/bottom_bar.hh [ 0%] Built target ost_img_headers [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vec3.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/src/vec3.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./input.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./input.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_mae_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./xcs_editor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./xcs_editor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_mmcif_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/button_box.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/button_box.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bounding_box.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./bounding_box.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./prim_list.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./prim_list.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./scene.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./scene.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/event_button.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/event_button.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./selection.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./selection.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./transform.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./transform.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./pdb_reader.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_widget_container.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/panel_widget_container.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_pdb_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_pdb_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./surface.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./surface.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_writer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./pdb_writer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar_widget_holder.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/panel_bar_widget_holder.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./texture.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./texture.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_sdf_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/side_bar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/side_bar.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./vertex_array.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./vertex_array.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/sdf_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./sdf_reader.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/splitter_panel_bar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/splitter_panel_bar.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./vertex_array_helper.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/sdf_writer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./sdf_writer.hh [ 1%] Built target ost_mol_headers cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/tabbed_panel_bar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/tabbed_panel_bar.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./scene_observer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./scene_observer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/context_menu.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/save_entity.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./save_entity.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/current_selection_node.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat2_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/src/vecmat2_op.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gl_include.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gl_include.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/load_entity.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./load_entity.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./glext_include.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./glext_include.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/custom_part_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./render_mode.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./render_mode.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/surface_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./surface_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/entity_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./material.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./material.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/load_surface.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./load_surface.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/entity_part_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/surface_io_msms_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gradient.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gradient.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/gfx_scene_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gradient_manager.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gradient_manager.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_str.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./pdb_str.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/stereochemical_params_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/label_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/label_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/omf.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./omf.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/sequence_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./primitives.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./primitives.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/root_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/fasta_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./povray_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./povray_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/pir_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./pir_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/render_mode_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/render_modes_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./povray.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./povray.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/promod_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./promod_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/profile_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./profile_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./exporter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./exporter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/hhm_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./hhm_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./exporter_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./exporter_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gost_exporter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gost_exporter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/message_widget.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/messages/message_widget.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/pssm_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./pssm_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./color_ops/map_handle_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./map_handle_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_iso.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./map_iso.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/clustal_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./clustal_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/messages/message_box_widget.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_slab.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./map_slab.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/load.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./load.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/log_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/messages/log_reader.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_iso_prop.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./map_iso_prop.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/argand.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/argand.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/save.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./save.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh [ 1%] Built target ost_gfx_headers cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/load_map.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./load_map.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat3_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/src/vecmat3_op.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_df3_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_df3_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/image_format.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./image_format.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/draw_overlay.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dx_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_dx_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/drawing_functions.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_spi_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_spi_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/fft_panel.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_situs_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_situs_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/info_panel.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_mrc_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_mrc_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/img2qt.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/mask_overlay.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dat_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_dat_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_ipl_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_ipl_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/null_overlay.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/null_overlay.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_jpk_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_jpk_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_nanoscope_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_nanoscope_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_png_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_png_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dm3_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_dm3_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_gui.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_gui.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_tiff_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_tiff_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/tiff_util.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./tiff_util.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_observer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_observer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/jpk_util.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./jpk_util.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay_base.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/strategies.hh [ 1%] Built target ost_io_headers cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/strategies_fw.hh [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/vecmat4_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/src/vecmat4_op.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/viewer_normalizer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_browser.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./file_browser.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_type_dialog.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./file_type_dialog.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_viewer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./file_viewer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gl_canvas.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./gl_canvas.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gl_win.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./gl_win.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./scene_menu.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./scene_menu.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gosty_app.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./gosty_app.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./admin.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./admin.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./main.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main_area.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./main_area.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./perspective.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./perspective.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./scene_selection.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./scene_selection.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main_window.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./main_window.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./dock_widget.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./dock_widget.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./dock_widget.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./dock_widget.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./thin_splitter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./thin_splitter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_geom_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget_geom_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_pool.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget_pool.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_registry.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget_registry.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_state_saver.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget_state_saver.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_loader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./file_loader.hh make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 1%] Built target ost_gui_headers [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite2.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/src/composite2.cc In file included from /build/openstructure-2.3.1/modules/geom/src/composite2.hh:27, from /build/openstructure-2.3.1/modules/geom/src/composite2.cc:23: /build/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/openstructure-2.3.1/modules/geom/src/def.hh:26, from /build/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/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.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/src/composite2_op.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/composite3_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/src/quat.cc [ 1%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/transform.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/src/aligned_cuboid.cc [ 2%] Building CXX object modules/geom/src/CMakeFiles/ost_geom.dir/point_cloud.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/c++ -DOST_MODULE_OST_GEOM -Dost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/src/point_cloud.cc /build/openstructure-2.3.1/modules/geom/src/composite3.cc: In member function 'geom::Quat geom::Rotation3::GetQuat() const': /build/openstructure-2.3.1/modules/geom/src/composite3.cc:218:27: note: parameter passing for argument of type 'geom::Quat' when C++17 is enabled changed to match C++14 in GCC 10.1 218 | Quat Rotation3::GetQuat() const | ^~~~~ In file included from /build/openstructure-2.3.1/modules/geom/src/composite2.hh:27, from /build/openstructure-2.3.1/modules/geom/src/composite2_op.hh:24, from /build/openstructure-2.3.1/modules/geom/src/composite2_op.cc:24: /build/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/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/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 | ^~~~~~~~ /build/openstructure-2.3.1/modules/geom/src/quat.cc: In function 'geom::Quat geom::{anonymous}::extract_from_rotmat(const geom::Mat3&)': /build/openstructure-2.3.1/modules/geom/src/quat.cc:185:41: note: parameter passing for argument of type 'geom::Quat' when C++17 is enabled changed to match C++14 in GCC 10.1 185 | Quat extract_from_rotmat(const Mat3& rot) | ^ [ 2%] Linking CXX shared library ../../../stage/lib/libost_geom.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: /usr/lib/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 2%] Built target ost_geom make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src/CMakeFiles/ost_base.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod/CMakeFiles/_ost_geom.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/generic_property.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/src/generic_property.cc make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 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/units.cc.o [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/log_sink.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/src/log_sink.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/src/units.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/src/log.cc [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/string_ref.cc.o [ 2%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/profile.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/src/string_ref.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/src/profile.cc [ 3%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/platform.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/src/platform.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec2.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/pymod/export_vec2.cc [ 5%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/message.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/src/message.cc [ 5%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/test_utils/compare_files.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/src/test_utils/compare_files.cc [ 5%] Building CXX object modules/base/src/CMakeFiles/ost_base.dir/boost_filesystem_helper.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/c++ -DOST_MODULE_OST_BASE -Dost_base_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/src/boost_filesystem_helper.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat2_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/pymod/export_vecmat2_op.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec3.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/pymod/export_vec3.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat3_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/pymod/export_vecmat3_op.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vec4.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/pymod/export_vec4.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_vecmat4_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/pymod/export_vecmat4_op.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/wrap_geom.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/pymod/wrap_geom.cc [ 5%] Linking CXX shared library ../../../stage/lib/libost_base.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 5%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src/CMakeFiles/ost_info.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 5%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_impl.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/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 /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_vec2.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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/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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat2_op.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat3_op.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_vec3.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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 /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/info/src/info_impl.hh:41, from /build/openstructure-2.3.1/modules/info/src/info_impl.cc:37: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_vec4.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_vecmat4_op.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/wrap_geom.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_mat2.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/pymod/export_mat2.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat3.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/pymod/export_mat3.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_mat4.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/pymod/export_mat4.cc [ 5%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/pymod/export_composite2.cc [ 6%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_mat2.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_mat3.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_mat4.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_composite2.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite2_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/pymod/export_composite2_op.cc [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_handle.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/info/src/info_handle.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/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( | ^~~~~~~~~~~~~~~~~~~~ /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_composite3.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/geom/pymod/CMakeFiles/_ost_geom.dir/export_composite3_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/pymod/export_composite3_op.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/info/src/info_group.hh:33, from /build/openstructure-2.3.1/modules/info/src/info.hh:32, from /build/openstructure-2.3.1/modules/info/src/info_handle.cc:30: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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( | ^~~~~~~~~~~~~~~~~~~~ In file included from /usr/include/boost/preprocessor/iteration/detail/iter/forward1.hpp:47, from /usr/include/boost/python/detail/invoke.hpp:61, from /usr/include/boost/python/detail/caller.hpp:16, from /usr/include/boost/python/object/function_handle.hpp:8, from /usr/include/boost/python/converter/arg_to_python.hpp:19: /usr/include/boost/python/detail/invoke.hpp: In function 'PyObject* boost::python::detail::invoke(invoke_tag_, const RC&, F&, TC&) [with RC = boost::python::to_python_value; F = geom::Quat (geom::Rotation3::*)() const; TC = boost::python::arg_from_python]': /usr/include/boost/python/detail/invoke.hpp:86:25: note: parameter passing for argument of type 'geom::Quat' when C++17 is enabled changed to match C++14 in GCC 10.1 86 | return rc( (tc().*f)(BOOST_PP_ENUM_BINARY_PARAMS_Z(1, N, ac, () BOOST_PP_INTERCEPT)) ); | ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 6%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_quat.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/pymod/export_quat.cc [ 6%] Building CXX object modules/geom/pymod/CMakeFiles/_ost_geom.dir/export_transform.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/c++ -D_ost_geom_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/geom/pymod/export_transform.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_composite2_op.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/info/src/CMakeFiles/ost_info.dir/info_group.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_item.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/info/src/info_item.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_composite3_op.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/info/src/CMakeFiles/ost_info.dir/info_path.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/info/src/info_path.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/info/src/info_group.hh:33, from /build/openstructure-2.3.1/modules/info/src/info.hh:32, from /build/openstructure-2.3.1/modules/info/src/info_group.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/modules/info/src/info_handle.hh:31, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/pymod/export_quat.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/modules/geom/pymod/export_quat.cc: In function 'geom::Quat normalize(const geom::Quat&)': /build/openstructure-2.3.1/modules/geom/pymod/export_quat.cc:24:42: note: parameter passing for argument of type 'geom::Quat' when C++17 is enabled changed to match C++14 in GCC 10.1 24 | geom::Quat normalize (const geom::Quat& q) | ^ [ 6%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_set.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/info/src/info_set.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/info/src/info_group.hh:33, from /build/openstructure-2.3.1/modules/info/src/info.hh:32, from /build/openstructure-2.3.1/modules/info/src/info_item.cc:31: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/info/src/CMakeFiles/ost_info.dir/info_visitor.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/info/src/info_visitor.cc [ 7%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/geom_info_conversion.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/info/src/geom_info_conversion.cc [ 7%] Building CXX object modules/info/src/CMakeFiles/ost_info.dir/info_verbose_visitor.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/info/src/info_verbose_visitor.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/info/src/info_group.hh:33, from /build/openstructure-2.3.1/modules/info/src/info_set.hh:29, from /build/openstructure-2.3.1/modules/info/src/info_set.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/info/src/geom_info_conversion.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info_handle.hh:31, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/info/src/info_group.hh:33, from /build/openstructure-2.3.1/modules/info/src/info_verbose_visitor.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/geom/_ost_geom.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so /usr/lib/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/geom/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/geom/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 7%] Built target _ost_geom make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod/CMakeFiles/_ost_base.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 7%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/wrap_base.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/pymod/wrap_base.cc [ 7%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_range.cc.o [ 7%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_units.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/pymod/export_range.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/pymod/export_units.cc [ 7%] Building CXX object modules/base/pymod/CMakeFiles/_ost_base.dir/export_logger.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/c++ -D_ost_base_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/pymod/export_logger.cc [ 7%] Linking CXX shared library ../../../stage/lib/libost_info.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 ../../../stage/lib/libost_base.so.2.3.1 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 7%] 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[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_base.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/atom_base.cc [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/composite_mask.cc.o [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/circle_mask.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/composite_mask.cc cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/circle_mask.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_handle.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/atom_handle.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, from /build/openstructure-2.3.1/modules/img/base/src/composite_mask.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/composite_mask.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/circle_mask.hh:25, from /build/openstructure-2.3.1/modules/img/base/src/circle_mask.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/atom_handle.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/atom_handle.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh:24, from /build/openstructure-2.3.1/modules/mol/base/src/atom_base.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/atom_base.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/data_algorithm.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/data_algorithm.cc [ 7%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data_observer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/data_observer.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/atom_view.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/atom_view.cc [ 7%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bond_handle.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/bond_handle.cc [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_base.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/chain_base.cc [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/data.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/data.cc [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_handle.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/chain_handle.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/data.hh:36, from /build/openstructure-2.3.1/modules/img/base/src/image_handle.hh:38, from /build/openstructure-2.3.1/modules/img/base/src/data_observer.hh:31, from /build/openstructure-2.3.1/modules/img/base/src/data_observer.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/data.hh:36, from /build/openstructure-2.3.1/modules/img/base/src/data.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/modules/mol/base/src/residue_view.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/atom_view.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/atom_view.hh:25, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, from /build/openstructure-2.3.1/modules/mol/base/src/bond_handle.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/bond_handle.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/chain_base.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/chain_base.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_iterator.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/extent_iterator.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/chain_handle.cc:24: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 8%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent_mask.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/extent_mask.cc [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_view.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/chain_view.cc [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/chain_type.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/chain_type.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/extent_iterator.hh:30, from /build/openstructure-2.3.1/modules/img/base/src/extent_iterator.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/extent.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/extent_mask.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/extent_mask.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/mol/base/src/CMakeFiles/ost_mol.dir/coord_frame.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/coord_frame.cc [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_group.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/coord_group.cc [ 8%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/editor_base.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/editor_base.cc [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/extent.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/extent.cc [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_factory.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/image_factory.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/chain_view.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/editor_base.hh:27, from /build/openstructure-2.3.1/modules/mol/base/src/editor_base.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/in_mem_coord_source.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/coord_frame.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/coord_group.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/entity_base.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/entity_base.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/extent.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/extent.cc:31: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/editor_base.cc:22: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/extent.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/image_factory.hh:32, from /build/openstructure-2.3.1/modules/img/base/src/image_factory.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_handle.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/image_handle.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_handle.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/entity_handle.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/entity_base.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/entity_base.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 10%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_impl.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/image_impl.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_observer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/entity_observer.cc [ 10%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_property_mapper.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/entity_view.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/entity_view.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/data.hh:36, from /build/openstructure-2.3.1/modules/img/base/src/image_handle.hh:38, from /build/openstructure-2.3.1/modules/img/base/src/image_handle.cc:31: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/entity_visitor.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/entity_visitor.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/entity_handle.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh:31, from /build/openstructure-2.3.1/modules/img/base/src/image_state_fw.hh:30, from /build/openstructure-2.3.1/modules/img/base/src/image_impl.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/image_impl.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41: /build/openstructure-2.3.1/obj-aarch64-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/ics_editor.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/ics_editor.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.hh:29, from /build/openstructure-2.3.1/modules/mol/base/src/entity_property_mapper.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/not_connected_error.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/not_connected_error.cc [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_list.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/image_list.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.hh:32, from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:30: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:40: /build/openstructure-2.3.1/obj-aarch64-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/inverted_mask.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/inverted_mask.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/image_list.hh:29, from /build/openstructure-2.3.1/modules/img/base/src/image_list.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/ics_editor.cc:24: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc: In member function 'std::pair ost::mol::EntityView::GetMinMax(const String&, ost::mol::Prop::Level) const': /build/openstructure-2.3.1/modules/mol/base/src/entity_view.cc:663:62: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 663 | Prop::Level hint) const | ^~~~~ [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/property_id.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/property_id.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, from /build/openstructure-2.3.1/modules/img/base/src/inverted_mask.hh:23, from /build/openstructure-2.3.1/modules/img/base/src/inverted_mask.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/query.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/query.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_error.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/query_error.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_state.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/query_state.cc [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/map.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/map.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_base.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/residue_base.cc [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_base.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/mask_base.cc [ 11%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/residue_handle.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/residue_handle.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/map.hh:22, from /build/openstructure-2.3.1/modules/img/base/src/map.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/query_state.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/query.hh:39, from /build/openstructure-2.3.1/modules/mol/base/src/query.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/query_state.cc:24: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, from /build/openstructure-2.3.1/modules/img/base/src/mask_base.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/residue_base.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/residue_base.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/mask_op.cc [ 11%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/mask.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/residue_handle.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/residue_handle.cc:26: /build/openstructure-2.3.1/obj-aarch64-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/residue_view.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/residue_view.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/mask_base.hh:27, from /build/openstructure-2.3.1/modules/img/base/src/composite_mask.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/mask_op.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/modules/img/base/src/mask_base_fw.hh:23, from /build/openstructure-2.3.1/modules/img/base/src/mask_op.hh:24, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/mask.hh:29, from /build/openstructure-2.3.1/modules/img/base/src/mask.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_builder.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/surface_builder.cc [ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/surface_handle.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/surface_handle.cc [ 12%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/transfer_connectivity.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.cc [ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/observable.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/observable.cc [ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/paste_impl.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/paste_impl.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/modules/mol/base/src/residue_view.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/surface_handle.hh:24, from /build/openstructure-2.3.1/modules/mol/base/src/surface_builder.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/surface_builder.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/observable.hh:31, from /build/openstructure-2.3.1/modules/img/base/src/observable.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/openstructure-2.3.1/modules/mol/base/src/surface_handle.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/query.hh:39, from /build/openstructure-2.3.1/modules/mol/base/src/entity_handle.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.hh:24, from /build/openstructure-2.3.1/modules/mol/base/src/transfer_connectivity.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/module_config.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_algorithm.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/paste_impl.hh:24, from /build/openstructure-2.3.1/modules/img/base/src/paste_impl.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/peak.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/peak.cc [ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/torsion_handle.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/torsion_handle.cc [ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/query_view_wrapper.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/query_view_wrapper.cc [ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/view_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/view_op.cc [ 14%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/_ost_base.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_base.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/settings.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./settings.pyc\",\"settings.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/stutil.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./stutil.pyc\",\"stutil.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/table.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table.pyc\",\"table.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/table_selector.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./table_selector.pyc\",\"table_selector.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/xmlrunner.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./xmlrunner.pyc\",\"xmlrunner.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/base/pymod/testutils.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/./testutils.pyc\",\"testutils.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 14%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/pymod/CMakeFiles/_ost_info.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/peak.hh:31, from /build/openstructure-2.3.1/modules/img/base/src/peak.cc:30: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 14%] Building CXX object modules/info/pymod/CMakeFiles/_ost_info.dir/wrap_info.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/info/pymod/wrap_info.cc [ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/coord_source.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/coord_source.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh:24, from /build/openstructure-2.3.1/modules/mol/base/src/torsion_handle.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/torsion_handle.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/in_mem_coord_source.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/modules/mol/base/src/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/modules/mol/base/src/query_view_wrapper.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 14%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/phase.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/phase.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/view_op.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/view_op.cc:27: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/bounding_box.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/bounding_box.cc /build/openstructure-2.3.1/modules/img/base/src/phase.cc: In member function 'const ost::img::Phase ost::img::Phase::operator+=(const ost::img::Phase&)': /build/openstructure-2.3.1/modules/img/base/src/phase.cc:49:47: note: parameter passing for argument of type 'ost::img::Phase' when C++17 is enabled changed to match C++14 in GCC 10.1 49 | const Phase Phase::operator+=(const Phase& rhs) | ^ [ 14%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/xcs_editor.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/xcs_editor.cc [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_impl.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc [ 15%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/physical_units.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/physical_units.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/in_mem_coord_source.cc:1: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/coord_source.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/pixel_sampling.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/pixel_sampling.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/xcs_editor.cc:26: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.cc:27: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/info/pymod/wrap_info.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log_sink.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:25, from /build/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( | ^~~~~~~~~~~~~~~~~~~~ [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/chain_impl.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/connector_impl.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/pixel_sampling.hh:32, from /build/openstructure-2.3.1/modules/img/base/src/pixel_sampling.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/bounding_box.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/mol/base/src/CMakeFiles/ost_mol.dir/impl/dihedral.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.cc [ 15%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/point_list.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/point_list.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.hh:24, from /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.cc:23: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.cc:24: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/entity_impl.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/impl/entity_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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log_sink.hh:29, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.cc:21: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/point_list.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/point_list.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/mol/base/src/CMakeFiles/ost_mol.dir/impl/fragment_impl.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.cc [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_ast.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/impl/query_ast.cc [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/query_impl.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc:35: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/point.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/point.cc In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.cc:40: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 15%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/residue_impl.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/point.cc:31: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/mol/base/src/CMakeFiles/ost_mol.dir/impl/surface_impl.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh:36, from /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/mol/base/src/CMakeFiles/ost_mol.dir/impl/torsion_impl.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc [ 15%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/polygon_mask.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/polygon_mask.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.cc:25: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log_sink.hh:29, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/polygon_mask.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh:25, from /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.cc:27: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 15%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/progress.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/progress.cc [ 16%] Building CXX object modules/mol/base/src/CMakeFiles/ost_mol.dir/impl/atom_prop.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/src/impl/atom_prop.cc [ 16%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/size.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/size.cc [ 17%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/spherical_mask.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/spherical_mask.cc [ 17%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/mask_info_convert.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/mask_info_convert.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/src/size.cc:32: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/spherical_mask.hh:28, from /build/openstructure-2.3.1/modules/img/base/src/spherical_mask.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/base/src/CMakeFiles/ost_img.dir/image_state/image_state_factory.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.cc [ 17%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/index.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/image_state/index.cc [ 17%] Building CXX object modules/img/base/src/CMakeFiles/ost_img.dir/image_state/image_state_base.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/img/base/src/mask_info_convert.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/base/src/CMakeFiles/ost_img.dir/raster_image/raster_image.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh:31, from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data_types.hh:30, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh:34, from /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base_fw.hh:28, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.hh:31, from /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.cc:38: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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%] Linking CXX shared library ../../../../stage/lib/libost_mol.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 17%] Built target ost_mol make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 17%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_impl.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.cc [ 17%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_column.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/base/src/aligned_column.cc [ 17%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/impl/sequence_list_impl.cc.o [ 17%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/aligned_region.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/base/src/aligned_region.cc [ 17%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_handle.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.cc cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/base/src/sequence_handle.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/modules/seq/base/src/sequence_handle.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info_handle.hh:31, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:26, from /build/openstructure-2.3.1/modules/seq/base/src/aligned_region.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/integrity_error.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/openstructure-2.3.1/modules/seq/base/src/aligned_column.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/seq/base/src/CMakeFiles/ost_seq.dir/sequence_list.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/seq/base/src/CMakeFiles/ost_seq.dir/alignment_handle.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/base/src/alignment_handle.cc [ 17%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/sequence_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/base/src/sequence_op.cc [ 17%] Linking CXX shared library ../../../../stage/lib/libost_img.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 [ 17%] Building CXX object modules/seq/base/src/CMakeFiles/ost_seq.dir/views_from_sequences.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/base/src/views_from_sequences.cc cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 17%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/anisotropic.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/anisotropic.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/seq/base/src/sequence_list.cc:31: /build/openstructure-2.3.1/obj-aarch64-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/seq/base/src/CMakeFiles/ost_seq.dir/profile_handle.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/base/src/profile_handle.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/modules/seq/base/src/alignment_handle.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/invalid_handle.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/seq/base/src/alignment_handle.cc:27: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/openstructure-2.3.1/modules/seq/base/src/alignment_handle.cc:32: /build/openstructure-2.3.1/obj-aarch64-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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/views_from_sequences.hh:23, from /build/openstructure-2.3.1/modules/seq/base/src/views_from_sequences.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/integrity_error.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian.hh:36, from /build/openstructure-2.3.1/modules/img/alg/src/anisotropic.hh:28, from /build/openstructure-2.3.1/modules/img/alg/src/anisotropic.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/info/_ost_info.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/info/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/info/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 17%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 17%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_atom.cc [ 17%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_atom_view.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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_view.cc.o -MF CMakeFiles/_ost_mol.dir/export_atom_view.cc.o.d -o CMakeFiles/_ost_mol.dir/export_atom_view.cc.o -c /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom_view.cc [ 17%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bond.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_bond.cc [ 17%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_chain.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/auto_correlate.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/convolute.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/convolute.cc [ 17%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/correlate.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/correlate.cc [ 19%] Linking CXX shared library ../../../../stage/lib/libost_seq.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 19%] Built target ost_seq 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/pymod/CMakeFiles/_ost_img.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 19%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_data.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/pymod/export_data.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/fft.hh:27, from /build/openstructure-2.3.1/modules/img/alg/src/auto_correlate.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/convolute.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/convolute.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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 /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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/correlate.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/correlate.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/cross_correlate.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/cross_correlate.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_atom_view.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_bond.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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 /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/cross_correlate.hh:27, from /build/openstructure-2.3.1/modules/img/alg/src/cross_correlate.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/modules/img/base/pymod/export_data.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/density_slice.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/density_slice.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/dft.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/dft.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/fft.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/fft.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/density_slice.hh:28, from /build/openstructure-2.3.1/modules/img/alg/src/density_slice.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/dft.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/dft.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/base/pymod/CMakeFiles/_ost_img.dir/export_data_algorithm.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/pymod/export_data_algorithm.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/fft.cc:36: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/fourier_filters.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/fourier_filters.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/gaussian.cc [ 20%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_chain_view.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_chain_view.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/gaussian_gradient_magnitude.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, from /build/openstructure-2.3.1/modules/img/alg/src/fourier_filters.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian.hh:36, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian_gradient_magnitude.hh:28, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian_gradient_magnitude.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/base/pymod/export_data_algorithm.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/gaussian_laplacian.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_chain_view.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/highest_peak_search_3d.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/highest_peak_search_3d.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/histogram.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/histogram.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.hh:28, from /build/openstructure-2.3.1/modules/img/alg/src/gaussian_laplacian.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, from /build/openstructure-2.3.1/modules/img/alg/src/highest_peak_search_3d.cc:4: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/stat.hh:30, from /build/openstructure-2.3.1/modules/img/alg/src/histogram.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_group.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_coord_group.cc [ 20%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_iterator.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/line_iterator.cc [ 20%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_extent.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/pymod/export_extent.cc [ 20%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_coord_frame.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_coord_frame.cc [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/local_sigma_threshold.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/img/alg/src/line_iterator.hh:29, from /build/openstructure-2.3.1/modules/img/alg/src/line_iterator.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/mask_image.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/mask_image.cc [ 21%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_editors.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/normalizer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/normalizer.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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/local_sigma_threshold.hh:23, from /build/openstructure-2.3.1/modules/img/alg/src/local_sigma_threshold.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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 /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_group.hh:29, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_group.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/img/base/pymod/wrap_extent_iterator.hh:34, from /build/openstructure-2.3.1/modules/img/base/pymod/export_extent.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/mask_image.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_coord_frame.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/normalizer_factory.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/normalizer_factory.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/normalizer.hh:28, from /build/openstructure-2.3.1/modules/img/alg/src/normalizer.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/norm_linear.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/norm_linear.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 21%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_log.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/norm_log.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/stat_min_max.hh:30, from /build/openstructure-2.3.1/modules/img/alg/src/normalizer_factory.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_editors.cc:25: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 23%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/norm_linear.hh:28, from /build/openstructure-2.3.1/modules/img/alg/src/norm_linear.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/norm_log.hh:28, from /build/openstructure-2.3.1/modules/img/alg/src/norm_log.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 23%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/norm_od.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/norm_od.cc [ 23%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_entity_view.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_entity_view.cc [ 23%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_property_id.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_property_id.cc [ 23%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/power_spectrum.cc [ 23%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/randomize.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/randomize.cc [ 23%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_handle.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/pymod/export_image_handle.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/norm_od.hh:28, from /build/openstructure-2.3.1/modules/img/alg/src/norm_od.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/fft.hh:27, from /build/openstructure-2.3.1/modules/img/alg/src/power_spectrum.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/randomize.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/randomize.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 23%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/smooth_mask_image.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh:41, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity.cc:24: /build/openstructure-2.3.1/obj-aarch64-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 /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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ /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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 24%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/stat.cc [ 24%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/stat_min_max.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_property_id.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_view.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/base/pymod/export_image_handle.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/smooth_mask_image.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/stat_min_max.hh:30, from /build/openstructure-2.3.1/modules/img/alg/src/stat_min_max.cc:32: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/stat.hh:30, from /build/openstructure-2.3.1/modules/img/alg/src/stat.cc:32: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/alg/src/CMakeFiles/ost_img_alg.dir/alg_transform.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/alg_transform.cc [ 24%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_query.cc [ 24%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_residue.cc [ 24%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/alg_mirror.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/alg_transform.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/alg_transform.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/alg_mirror.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/alg_mirror.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/alg/src/CMakeFiles/ost_img_alg.dir/alg_shift.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/alg_shift.cc [ 24%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/threshold.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/threshold.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/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( | ^~~~~~~~~~~~~~~~~~~~ /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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_query.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/alg/src/CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/alg_shift.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/alg_shift.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/threshold.hh:25, from /build/openstructure-2.3.1/modules/img/alg/src/threshold.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/discrete_shrink.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/alg/src/CMakeFiles/ost_img_alg.dir/transformation_base.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/transformation_base.cc [ 24%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/transformations.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/transformations.cc [ 24%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_residue_view.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_residue_view.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/modules/img/alg/src/transformation_base.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/transformations.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/transformations.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/alg/src/CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/fractional_shift.cc [ 24%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/polar.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/polar.cc [ 25%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/rscrosscorr.cc [ 26%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_peak.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/pymod/export_peak.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, from /build/openstructure-2.3.1/modules/img/alg/src/fractional_shift.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/alg/src/polar.hh:24, from /build/openstructure-2.3.1/modules/img/alg/src/polar.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/src/rscrosscorr.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_surface.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 26%] Building CXX object modules/img/alg/src/CMakeFiles/ost_img_alg.dir/line_average.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/src/line_average.cc [ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_bounding_box.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_bounding_box.cc [ 26%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_query_view_wrapper.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_query_view_wrapper.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_residue_view.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/img/alg/src/line_average.hh:23, from /build/openstructure-2.3.1/modules/img/alg/src/line_average.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/peak.hh:31, from /build/openstructure-2.3.1/modules/img/base/pymod/export_peak.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_surface.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/mol/base/pymod/CMakeFiles/_ost_mol.dir/export_torsion.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_torsion.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/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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 26%] Linking CXX shared library ../../../../stage/lib/libost_img_alg.so cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_img_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-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_alg.so.2.3 -o ../../../../stage/lib/libost_img_alg.so.2.3.1 CMakeFiles/ost_img_alg.dir/anisotropic.cc.o CMakeFiles/ost_img_alg.dir/auto_correlate.cc.o CMakeFiles/ost_img_alg.dir/convolute.cc.o CMakeFiles/ost_img_alg.dir/correlate.cc.o CMakeFiles/ost_img_alg.dir/cross_correlate.cc.o CMakeFiles/ost_img_alg.dir/density_slice.cc.o CMakeFiles/ost_img_alg.dir/dft.cc.o CMakeFiles/ost_img_alg.dir/fft.cc.o CMakeFiles/ost_img_alg.dir/fourier_filters.cc.o CMakeFiles/ost_img_alg.dir/gaussian.cc.o CMakeFiles/ost_img_alg.dir/gaussian_gradient_magnitude.cc.o CMakeFiles/ost_img_alg.dir/gaussian_laplacian.cc.o CMakeFiles/ost_img_alg.dir/highest_peak_search_3d.cc.o CMakeFiles/ost_img_alg.dir/histogram.cc.o CMakeFiles/ost_img_alg.dir/line_iterator.cc.o CMakeFiles/ost_img_alg.dir/local_sigma_threshold.cc.o CMakeFiles/ost_img_alg.dir/mask_image.cc.o CMakeFiles/ost_img_alg.dir/normalizer.cc.o CMakeFiles/ost_img_alg.dir/normalizer_factory.cc.o CMakeFiles/ost_img_alg.dir/norm_linear.cc.o CMakeFiles/ost_img_alg.dir/norm_log.cc.o CMakeFiles/ost_img_alg.dir/norm_od.cc.o CMakeFiles/ost_img_alg.dir/power_spectrum.cc.o CMakeFiles/ost_img_alg.dir/randomize.cc.o CMakeFiles/ost_img_alg.dir/smooth_mask_image.cc.o CMakeFiles/ost_img_alg.dir/stat.cc.o CMakeFiles/ost_img_alg.dir/stat_min_max.cc.o CMakeFiles/ost_img_alg.dir/alg_transform.cc.o CMakeFiles/ost_img_alg.dir/alg_mirror.cc.o CMakeFiles/ost_img_alg.dir/alg_shift.cc.o CMakeFiles/ost_img_alg.dir/threshold.cc.o CMakeFiles/ost_img_alg.dir/discrete_shrink.cc.o CMakeFiles/ost_img_alg.dir/transformation_base.cc.o CMakeFiles/ost_img_alg.dir/transformations.cc.o CMakeFiles/ost_img_alg.dir/fractional_shift.cc.o CMakeFiles/ost_img_alg.dir/polar.cc.o CMakeFiles/ost_img_alg.dir/rscrosscorr.cc.o CMakeFiles/ost_img_alg.dir/line_average.cc.o -L/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_bounding_box.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img_alg.so.2.3 ../../../../stage/lib/libost_img_alg.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 26%] Built target ost_img_alg make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 26%] Building CXX object modules/bindings/src/CMakeFiles/ost_bindings.dir/wrap_tmalign.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/bindings/src/wrap_tmalign.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_query_view_wrapper.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/pymod/CMakeFiles/_ost_mol.dir/export_visitor.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_visitor.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/bindings/wrap_tmalign.hh:24, from /build/openstructure-2.3.1/modules/bindings/src/wrap_tmalign.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/modules/bindings/src/tmalign/param_set.h:6, from /build/openstructure-2.3.1/modules/bindings/src/tmalign/TMalign.h:4, from /build/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 | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 28%] Building CXX object modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/wrap_mol.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/wrap_mol.cc [ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_phase.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_visitor.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/pymod/CMakeFiles/_ost_mol.dir/export_entity_property_mapper.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/base/pymod/export_entity_property_mapper.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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ /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/python/type_id.hpp:11, from /usr/include/boost/python/instance_holder.hpp:11, from /usr/include/boost/python/object/pointer_holder.hpp:14, from /usr/include/boost/python/to_python_indirect.hpp:10, from /usr/include/boost/python/converter/arg_to_python.hpp:10: /usr/include/boost/operators.hpp: In instantiation of 'ost::img::Phase boost::operators_impl::operator+(const ost::img::Phase&, const ost::img::Phase&)': /usr/include/boost/python/operators.hpp:212:1: required from 'static PyObject* boost::python::detail::operator_l::apply::execute(lhs&, const rhs&) [with L = ost::img::Phase; R = ost::img::Phase; PyObject = _object; lhs = ost::img::Phase; rhs = ost::img::Phase]' /usr/include/boost/python/operators.hpp:154:15: required from 'void boost::python::detail::operator_::visit(ClassT&) const [with ClassT = boost::python::class_; boost::python::detail::operator_id id = boost::python::detail::op_add; L = boost::python::self_ns::self_t; R = boost::python::self_ns::self_t]' /usr/include/boost/python/def_visitor.hpp:31:34: required from 'static void boost::python::def_visitor_access::visit(const V&, classT&) [with V = boost::python::def_visitor >; classT = boost::python::class_]' /usr/include/boost/python/def_visitor.hpp:67:34: required from 'void boost::python::def_visitor::visit(classT&) const [with classT = boost::python::class_; DerivedVisitor = boost::python::detail::operator_]' /usr/include/boost/python/class.hpp:221:22: required from 'boost::python::class_::self& boost::python::class_::def(const boost::python::def_visitor&) [with Derived = boost::python::detail::operator_; W = ost::img::Phase; X1 = boost::python::detail::not_specified; X2 = boost::python::detail::not_specified; X3 = boost::python::detail::not_specified; self = boost::python::class_]' /build/openstructure-2.3.1/modules/img/base/pymod/export_phase.cc:40:9: required from here /usr/include/boost/operators.hpp:267:1: note: parameter passing for argument of type 'ost::img::Phase' when C++17 is enabled changed to match C++14 in GCC 10.1 267 | BOOST_BINARY_OPERATOR_COMMUTATIVE( addable, + ) | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/editor_base.hh:27, from /build/openstructure-2.3.1/modules/mol/base/pymod/wrap_mol.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/pymod/CMakeFiles/_ost_img.dir/export_point.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src/CMakeFiles/ost_db.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 28%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/sqlite_wrap.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/db/src/sqlite_wrap.cc [ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_progress.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/pymod/export_progress.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, from /build/openstructure-2.3.1/modules/mol/base/pymod/export_entity_property_mapper.cc:3: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/pymod/CMakeFiles/_ost_img.dir/export_raster_image.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/pymod/export_raster_image.cc [ 28%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/linear_indexer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/db/src/linear_indexer.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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point_list.hh:28, from /build/openstructure-2.3.1/modules/img/base/pymod/export_point.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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%] Linking CXX shared library ../../../stage/lib/libost_bindings.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 28%] Built target ost_bindings 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 28%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/clip_alignment.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/alg/src/clip_alignment.cc [ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_size.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/pymod/export_size.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 28%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/binary_container.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/db/src/binary_container.cc [ 28%] Building CXX object modules/db/src/CMakeFiles/ost_db.dir/extract_data_helper.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/db/src/extract_data_helper.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/raster_image/raster_image.hh:31, from /build/openstructure-2.3.1/modules/img/base/pymod/export_raster_image.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/pymod/CMakeFiles/_ost_img.dir/export_mask.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/pymod/export_mask.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/clip_alignment.hh:27, from /build/openstructure-2.3.1/modules/seq/alg/src/clip_alignment.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:24, from /build/openstructure-2.3.1/modules/db/src/extract_data_helper.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/mol/_ost_mol.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:27: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_image_list.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/pymod/export_image_list.cc [ 28%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/conservation.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/alg/src/conservation.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/base/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/./__init__.pyc\",\"__init__.py\",doraise=True)" 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 28%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 28%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_sequence.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc [ 28%] Building CXX object modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/export_profile_handle.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/base/pymod/export_profile_handle.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/pymod/export_size.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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%] Linking CXX shared library ../../../stage/lib/libost_db.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 28%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 28%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/processor.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/conop/src/processor.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/openstructure-2.3.1/modules/seq/alg/src/conservation.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/polygon_mask.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/mask.hh:29, from /build/openstructure-2.3.1/modules/img/base/pymod/export_mask.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/conop/src/processor.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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 /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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:34, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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); | ^~~~ [ 28%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/contact_prediction_score.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/alg/src/contact_prediction_score.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/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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 28%] Building CXX object modules/img/base/pymod/CMakeFiles/_ost_img.dir/export_map.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/base/pymod/export_map.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/base/pymod/export_image_list.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc:30: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc:34: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/openstructure-2.3.1/modules/seq/base/pymod/export_sequence.cc:37: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 28%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/distance_map.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/alg/src/distance_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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/map.hh:22, from /build/openstructure-2.3.1/modules/img/base/pymod/export_map.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/modules/img/base/pymod/wrap_img.cc:33: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/alg/src/CMakeFiles/ost_seq_alg.dir/entropy.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/alg/src/entropy.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/distance_map.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/distance_map.hh:33, from /build/openstructure-2.3.1/modules/seq/alg/src/distance_map.cc:25: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 28%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/amino_acids.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/amino_acids.cc.o -MF CMakeFiles/ost_conop.dir/amino_acids.cc.o.d -o CMakeFiles/ost_conop.dir/amino_acids.cc.o -c /build/openstructure-2.3.1/modules/conop/src/amino_acids.cc [ 28%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/conop.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/conop.cc.o -MF CMakeFiles/ost_conop.dir/conop.cc.o.d -o CMakeFiles/ost_conop.dir/conop.cc.o -c /build/openstructure-2.3.1/modules/conop/src/conop.cc [ 28%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/minimal_compound_lib.cc.o -MF CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o.d -o CMakeFiles/ost_conop.dir/minimal_compound_lib.cc.o -c /build/openstructure-2.3.1/modules/conop/src/minimal_compound_lib.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/modules/seq/alg/src/entropy.hh:24, from /build/openstructure-2.3.1/modules/seq/alg/src/entropy.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/modules/seq/alg/src/entropy.cc:24: /build/openstructure-2.3.1/obj-aarch64-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/stl_tree.h:63, from /usr/include/c++/12/set:60, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/alg/src/CMakeFiles/ost_seq_alg.dir/ins_del.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/alg/src/ins_del.cc [ 28%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/img/_ost_img.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/conop/src/compound_lib_base.hh:5, from /build/openstructure-2.3.1/modules/conop/src/minimal_compound_lib.hh:5, from /build/openstructure-2.3.1/modules/conop/src/minimal_compound_lib.cc:1: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/modules/conop/src/compound.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/img/base/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 28%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 29%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/wrap_alg.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/pymod/wrap_alg.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/modules/seq/alg/src/impl/align_impl.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/global_align.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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 | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 29%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound_lib_base.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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_base.cc.o -MF CMakeFiles/ost_conop.dir/compound_lib_base.cc.o.d -o CMakeFiles/ost_conop.dir/compound_lib_base.cc.o -c /build/openstructure-2.3.1/modules/conop/src/compound_lib_base.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/ins_del.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/modules/conop/src/compound.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/modules/seq/alg/src/impl/align_impl.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/local_align.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 29%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/diag.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/conop/src/diag.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/auto_correlate.hh:24, from /build/openstructure-2.3.1/modules/img/alg/pymod/wrap_alg.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/modules/seq/alg/src/merge_pairwise_alignments.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/merge_pairwise_alignments.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/conop/src/heuristic.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 29%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/rule_based.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/conop/src/rule_based.cc [ 30%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/pair_subst_weight_matrix.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/alg/src/pair_subst_weight_matrix.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/conop/src/diag.hh:23, from /build/openstructure-2.3.1/modules/conop/src/diag.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/seq/alg/src/CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/semiglobal_align.cc.o -MF CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o.d -o CMakeFiles/ost_seq_alg.dir/semiglobal_align.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/semiglobal_align.cc [ 32%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/model_check.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/conop/src/model_check.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/conop/src/rule_based.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 32%] Building CXX object modules/conop/src/CMakeFiles/ost_conop.dir/compound.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/conop/src/compound.cc [ 32%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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_identity.cc.o -MF CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o.d -o CMakeFiles/ost_seq_alg.dir/sequence_identity.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/sequence_identity.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/modules/seq/alg/src/impl/align_impl.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/semiglobal_align.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/modules/conop/src/model_check.hh:4, from /build/openstructure-2.3.1/modules/conop/src/model_check.cc:1: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/conop/src/model_check.cc:2: /build/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/bits/stl_algobase.h:65, from /usr/include/c++/12/vector:60, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 32%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/variance_map.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/variance_map.cc.o -MF CMakeFiles/ost_seq_alg.dir/variance_map.cc.o.d -o CMakeFiles/ost_seq_alg.dir/variance_map.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/variance_map.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_column_iterator.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/sequence_similarity.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh:26, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 32%] Building CXX object modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/hmm_score.cc.o -MF CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o.d -o CMakeFiles/ost_seq_alg.dir/hmm_score.cc.o -c /build/openstructure-2.3.1/modules/seq/alg/src/hmm_score.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/src/variance_map.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/distance_map.hh:33, from /build/openstructure-2.3.1/modules/seq/alg/src/variance_map.cc:31: /build/openstructure-2.3.1/obj-aarch64-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/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/openstructure-2.3.1/obj-aarch64-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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'void ost::GenericPropContainer::SetBoolProp(const String&, bool) [with H = ost::mol::BondHandle]': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc:93:21: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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 member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc:93:21: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc:93:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc:93:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc:121:23: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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 member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc:121:23: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc:121:23: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::AtomBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)' at /build/openstructure-2.3.1/modules/conop/src/ring_finder.cc:121:23: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In member function 'int ost::conop::RingFinder::VisitNext(ost::mol::AtomHandle&, ost::mol::AtomHandle&, std::map&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/hmm_score.hh:24, from /build/openstructure-2.3.1/modules/seq/alg/src/hmm_score.cc:1: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/profile_handle.hh:27, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 32%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_filter.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/pymod/export_filter.cc [ 32%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_normalizer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/pymod/export_normalizer.cc [ 32%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_transcendentals.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/pymod/export_transcendentals.cc [ 32%] Building CXX object modules/img/alg/pymod/CMakeFiles/_ost_img_alg.dir/export_polar.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/img/alg/pymod/export_polar.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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/gaussian.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/filter.hh:30, from /build/openstructure-2.3.1/modules/img/alg/pymod/export_filter.cc:30: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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 /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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 32%] Linking CXX shared library ../../../../stage/lib/libost_seq_alg.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 32%] Built target ost_seq_alg 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/transcendentals.hh:34, from /build/openstructure-2.3.1/modules/img/alg/pymod/export_transcendentals.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, from /build/openstructure-2.3.1/modules/img/alg/pymod/export_normalizer.cc:30: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/polar.hh:24, from /build/openstructure-2.3.1/modules/img/alg/pymod/export_polar.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 33%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/seq/_ost_seq.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/base/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 33%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/DependInfo.cmake --color= make -f modules/db/pymod/CMakeFiles/_ost_db.dir/build.make modules/db/pymod/CMakeFiles/_ost_db.dir/depend make -f modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build.make modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/pymod/CMakeFiles/_ost_db.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 33%] Building CXX object modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/wrap_seq_alg.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/seq/alg/pymod/wrap_seq_alg.cc [ 33%] Building CXX object modules/db/pymod/CMakeFiles/_ost_db.dir/export_linear_db.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/db/pymod/export_linear_db.cc [ 33%] Building CXX object modules/db/pymod/CMakeFiles/_ost_db.dir/wrap_db.cc.o [ 33%] Building CXX object modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/export_tmalign.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/db/pymod/wrap_db.cc [ 33%] Building CXX object modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/wrap_bindings.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/bindings/pymod/export_tmalign.cc cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/bindings/pymod/wrap_bindings.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 33%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/img/alg/_ost_img_alg.so cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_img_alg.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-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/openstructure-2.3.1/modules/seq/alg/pymod/wrap_seq_alg.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ /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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/img/alg/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/img/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 33%] Built target _ost_img_alg In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:24, from /build/openstructure-2.3.1/modules/db/pymod/export_linear_db.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/merge_pairwise_alignments.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/pymod/wrap_seq_alg.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/db/extract_data_helper.hh:27: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/ins_del.hh:25, from /build/openstructure-2.3.1/modules/seq/alg/pymod/wrap_seq_alg.cc:25: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 33%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/bindings/_ost_bindings.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_bindings.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/lga.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./lga.pyc\",\"lga.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/hbplus.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hbplus.pyc\",\"hbplus.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/msms.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./msms.pyc\",\"msms.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/tmtools.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./tmtools.pyc\",\"tmtools.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/dssp.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./dssp.pyc\",\"dssp.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/clustalw.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./clustalw.pyc\",\"clustalw.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/utils.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./utils.pyc\",\"utils.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/naccess.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./naccess.pyc\",\"naccess.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/hhblits.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits.pyc\",\"hhblits.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/hhblits2.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits2.pyc\",\"hhblits2.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/hhblits3.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./hhblits3.pyc\",\"hhblits3.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/blast.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./blast.pyc\",\"blast.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/cadscore.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./cadscore.pyc\",\"cadscore.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/kclust.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./kclust.pyc\",\"kclust.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/ialign.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./ialign.pyc\",\"ialign.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/bindings/pymod/mmseqs2.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/bindings/./mmseqs2.pyc\",\"mmseqs2.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 33%] Built target _ost_bindings [ 33%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/db/_ost_db.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 [ 33%] Linking CXX shared library ../../../stage/lib/libost_conop.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/db/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/db/./__init__.pyc\",\"__init__.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 33%] Built target _ost_db cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 33%] Built target ost_conop 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/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/conop/pymod/CMakeFiles/_ost_conop.dir/build.make modules/conop/pymod/CMakeFiles/_ost_conop.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/pymod/CMakeFiles/_ost_conop.dir/DependInfo.cmake --color= make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 33%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_compound.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/conop/pymod/export_compound.cc make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 33%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/wrap_conop.cc.o [ 33%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/svd_superpose.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/conop/pymod/wrap_conop.cc [ 33%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_heuristic.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/conop/pymod/export_heuristic.cc [ 33%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/bitmap_io.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/bitmap_io.cc [ 33%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_amino_acids.cc.o [ 34%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_processor.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/conop/pymod/export_amino_acids.cc cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/conop/pymod/export_processor.cc In file included from /usr/include/boost/bind.hpp:30, from /build/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( | ^~~~~~~~~~~~~~~~~~~~ [ 34%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/exporter.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/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/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/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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ /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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, from /build/openstructure-2.3.1/modules/mol/alg/src/svd_superpose.cc:30: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/conop/pymod/CMakeFiles/_ost_conop.dir/export_conop.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/conop/pymod/export_conop.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/processor.hh:22, from /build/openstructure-2.3.1/modules/conop/pymod/export_processor.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/heuristic.hh:22, from /build/openstructure-2.3.1/modules/conop/pymod/export_heuristic.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, from /build/openstructure-2.3.1/modules/conop/pymod/export_compound.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/amino_acids.hh:26, from /build/openstructure-2.3.1/modules/conop/pymod/export_amino_acids.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-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/stl_tree.h:63, from /usr/include/c++/12/map:60, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/collada_exporter.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/collada_exporter.cc [ 35%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_diag.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/conop/pymod/export_diag.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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/conop/pymod/export_conop.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/collada_exporter.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/conop/pymod/CMakeFiles/_ost_conop.dir/export_rule_based.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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_rule_based.cc.o -MF CMakeFiles/_ost_conop.dir/export_rule_based.cc.o.d -o CMakeFiles/_ost_conop.dir/export_rule_based.cc.o -c /build/openstructure-2.3.1/modules/conop/pymod/export_rule_based.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 35%] Building CXX object modules/conop/pymod/CMakeFiles/_ost_conop.dir/export_ring_finder.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/conop/pymod/export_ring_finder.cc [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/color.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/diag.hh:23, from /build/openstructure-2.3.1/modules/conop/pymod/export_diag.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/primitives.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/primitives.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/color.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/primitives.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/primitives.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/gl_helper.hh:36, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/entity.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/entity.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/rule_based.hh:22, from /build/openstructure-2.3.1/modules/conop/pymod/export_rule_based.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/symmetry_node.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/symmetry_node.cc [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_node.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/gfx_node.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/ring_finder.hh:27, from /build/openstructure-2.3.1/modules/conop/pymod/export_ring_finder.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/modules/gfx/src/entity.cc:36: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/symmetry_node.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/symmetry_node.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/gl_helper.hh:36, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/gfx_object.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/gfx_object.cc /build/openstructure-2.3.1/modules/gfx/src/entity.cc: In member function 'void ost::gfx::Entity::ColorBy(const String&, const ost::gfx::Color&, const ost::gfx::Color&, ost::mol::Prop::Level)': /build/openstructure-2.3.1/modules/gfx/src/entity.cc:965:72: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 965 | std::pair minmax = this->GetView().GetMinMax(prop, level); | ^ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/gfx_object_base.hh:26, from /build/openstructure-2.3.1/modules/gfx/src/gfx_object.hh:40, from /build/openstructure-2.3.1/modules/gfx/src/gfx_node.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/gfx_prim.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/gfx_prim.cc [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gfx_test_object.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/gfx_test_object.cc [ 35%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/conop/_ost_conop.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_conop.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so [ 35%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/seq/alg/_ost_seq_alg.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_seq_alg.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/conop/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/conop/pymod/cleanup.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/conop/./cleanup.pyc\",\"cleanup.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/alg/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" [ 35%] Built target _ost_conop [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/input.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/input.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/alg/pymod/mat.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./mat.pyc\",\"mat.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/alg/pymod/renumber.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./renumber.pyc\",\"renumber.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/seq/alg/pymod/aaindex.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/seq/alg/./aaindex.pyc\",\"aaindex.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 35%] Built target _ost_seq_alg [ 35%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/prim_list.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/prim_list.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/gfx_prim.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/gfx_prim.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/scene.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/scene.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/gfx_object.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/selection.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/selection.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/gfx_object_base.hh:26, from /build/openstructure-2.3.1/modules/gfx/src/gfx_object.hh:40, from /build/openstructure-2.3.1/modules/gfx/src/gfx_test_object.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/gfx_test_object.cc:31: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/mol/alg/src/CMakeFiles/ost_mol_alg.dir/clash_score.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/clash_score.cc In file included from /usr/include/boost/bind.hpp:30, from /build/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( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/prim_list.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/surface.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/surface.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/scene.cc:40: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/selection.hh:26, from /build/openstructure-2.3.1/modules/gfx/src/selection.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/gradient.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/gradient.cc [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gradient_manager.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/gradient_manager.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/modules/mol/alg/src/clash_score.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/vertex_array.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/vertex_array.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/gradient.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/gradient.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/surface.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/vertex_array_helper.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/vertex_array_helper.cc [ 37%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_structure_segments.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/sec_structure_segments.cc [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/material.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/material.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/gfx/src/gradient_manager.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/vertex_array.hh:34, from /build/openstructure-2.3.1/modules/gfx/src/vertex_array.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/vertex_array_helper.hh:23, from /build/openstructure-2.3.1/modules/gfx/src/vertex_array_helper.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/povray.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/povray.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/material.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/material.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/sec_structure_segments.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/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/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) | ^~~~~~~~~~~~~~ [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/gost_exporter.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/gost_exporter.cc [ 37%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/texture.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/texture.cc [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/color_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/povray.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/povray.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 38%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/local_dist_diff_test.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_element_color_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.cc [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/by_chain_color_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.cc [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/uniform_color_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/gost_exporter.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.hh:24, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc:4: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.hh:24, from /build/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.cc:6: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/modules/mol/alg/src/local_dist_diff_test.hh:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh: In member function 'std::pair ost::mol::alg::StereoChemicalBondViolation::GetAllowedRange() const': /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh:91:48: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | std::pair GetAllowedRange() const { return allowed_range_; } | ^ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.hh:23, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/dyn_cast.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_color_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.cc [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/entity_view_color_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.cc [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/basic_gradient_color_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.cc [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/gradient_level_color_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.cc [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_renderer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 38%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/entity_detail.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/cartoon_renderer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info_handle.hh:31, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/dyn_cast.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/view_op.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.hh:27, from /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/custom_renderer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/atom_view.hh:25, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/cpk_renderer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/debug_renderer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/simple_renderer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/sline_renderer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh:23, from /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, from /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh:24, from /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh:27, from /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, from /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity_fw.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_test_common.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/distance_test_common.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/line_trace_renderer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec3.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gl_helper.hh:36, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/backbone_trace.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/connect_renderer_base.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.cc [ 39%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer_base.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/distance_test_common.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/distance_test_common.cc:1: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh:26, from /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/mol/alg/src/CMakeFiles/ost_mol_alg.dir/distance_rmsd_test.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/mapped_property.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/gfx/src/CMakeFiles/ost_gfx.dir/impl/tabulated_trig.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/tabulated_trig.cc [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/trace_renderer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:2: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/distance_rmsd_test.hh:24, from /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:3: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh: In member function 'std::pair ost::mol::alg::StereoChemicalBondViolation::GetAllowedRange() const': /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh:91:48: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | std::pair GetAllowedRange() const { return allowed_range_; } | ^ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_property_mapper.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/gfx/src/CMakeFiles/ost_gfx.dir/impl/fast_spheres.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/gfx/src/CMakeFiles/ost_gfx.dir/render_options/render_options.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/render_options/render_options.cc [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_render_options.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/render_options/line_render_options.cc [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/custom_render_options.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/render_options/custom_render_options.cc [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cpk_render_options.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/render_options/cpk_render_options.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/gfx/src/CMakeFiles/ost_gfx.dir/render_options/simple_render_options.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.cc [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/sline_render_options.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/render_options/sline_render_options.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/render_options/render_options.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/input.hh:30, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/gfx/src/CMakeFiles/ost_gfx.dir/render_options/line_trace_render_options.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/render_options/line_trace_render_options.cc In file included from /usr/include/c++/12/bits/stl_algobase.h:64, 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/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.hh:26, from /build/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.cc:23: /usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = float&; _T2 = float&; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp2>::type = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp>::type = float]': /build/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.cc:81:31: required from here /usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 741 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ 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 = 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:215:34: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:216:34: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)' at /build/openstructure-2.3.1/modules/mol/alg/src/distance_rmsd_test.cc:217:34: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'std::pair ost::mol::alg::DistanceRMSDTest(const ost::mol::EntityView&, const GlobalRDMap&, Real, int, const String&)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 41%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/cartoon_render_options.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/render_options/cartoon_render_options.cc [ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/render_options/trace_render_options.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/render_options/trace_render_options.cc [ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/color_ops/map_handle_color_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.cc [ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_iso.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/map_iso.cc [ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/map_slab.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/map_slab.cc [ 42%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/superpose_frames.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/superpose_frames.cc In file included from /usr/include/eigen3/Eigen/Core:341, from /usr/include/eigen3/Eigen/QR:11, from /usr/include/eigen3/Eigen/SVD:11, from /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.cc:26: /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h: In function 'static void Eigen::internal::trmv_selector::run(const Lhs&, const Rhs&, Dest&, const typename Dest::Scalar&) [with Lhs = Eigen::Transpose, -1, -1, false>, -1, -1, false> >; Rhs = Eigen::Transpose, const Eigen::CwiseNullaryOp, const Eigen::Matrix >, const Eigen::Transpose, -1, -1, false>, -1, 1, true>, -1, 1, false> > > >; Dest = Eigen::Transpose, 1, -1, true>, 1, -1, false> >; int Mode = 6]': /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:332:12: warning: 'result' may be used uninitialized [-Wmaybe-uninitialized] 327 | internal::triangular_matrix_vector_product | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 328 | | ~~~~~~~~~ 332 | ::run(actualLhs.rows(),actualLhs.cols(), | ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 333 | actualLhs.data(),actualLhs.outerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 334 | actualRhsPtr,1, | ~~~~~~~~~~~~~~~ 335 | dest.data(),dest.innerStride(), | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 336 | actualAlpha); | ~~~~~~~~~~~~ /usr/include/eigen3/Eigen/src/Core/products/TriangularMatrixVector.h:105:24: note: by argument 5 of type 'const float*' to 'static void Eigen::internal::triangular_matrix_vector_product::run(Index, Index, const LhsScalar*, Index, const RhsScalar*, Index, ResScalar*, Index, const ResScalar&) [with Index = long int; int Mode = 6; LhsScalar = float; bool ConjLhs = false; RhsScalar = float; bool ConjRhs = false; int Version = 0]' declared here 105 | EIGEN_DONT_INLINE void triangular_matrix_vector_product | ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ [ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.cc [ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_s.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.cc [ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_iso_gen_o.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_o.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/discrete_shrink.hh:24, from /build/openstructure-2.3.1/modules/gfx/src/map_iso.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, from /build/openstructure-2.3.1/modules/gfx/src/map_slab.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/vertex_array.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/map_iso_prop.hh:26, from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_o.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/modules/gfx/src/map_slab.cc: In function 'std::pair ost::gfx::{anonymous}::calc_sr(float, float, float, float, float, float)': /build/openstructure-2.3.1/modules/gfx/src/map_slab.cc:182:53: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 182 | float cx, float cy) | ^ [ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/map_octree.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/map_octree.cc [ 42%] Building CXX object modules/gfx/src/CMakeFiles/ost_gfx.dir/impl/octree_isocont.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/superpose_frames.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 42%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/filter_clashes.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/filter_clashes.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.hh:22, from /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/modules/gfx/src/impl/map_octree.cc: In member function 'std::pair ost::gfx::impl::MapOctree::BuildOctreeRec(const ost::gfx::impl::OcRangeVector&, uint16_t, ost::img::image_state::RealSpatialImageState*, const ost::img::Extent&, ost::gfx::impl::OctreeNode&)': /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.cc:84:68: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 84 | OctreeNode& parent) | ^ [ 42%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/construct_cbeta.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/construct_cbeta.cc [ 43%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/trajectory_analysis.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/trajectory_analysis.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh:27, from /build/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/structure_analysis.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/structure_analysis.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/filter_clashes.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/alg/src/filter_clashes.cc:24: /build/openstructure-2.3.1/modules/mol/alg/src/filter_clashes.hh: In member function 'std::pair ost::mol::alg::StereoChemicalBondViolation::GetAllowedRange() const': /build/openstructure-2.3.1/modules/mol/alg/src/filter_clashes.hh:91:48: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | std::pair GetAllowedRange() const { return allowed_range_; } | ^ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/mol/alg/src/trajectory_analysis.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/construct_cbeta.cc:4: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/consistency_checks.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/consistency_checks.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/structure_analysis.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/pdbize.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/pdbize.cc [ 43%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/adjacency_bitmap.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/modules/mol/alg/src/consistency_checks.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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%] Linking CXX shared library ../../../stage/lib/libost_gfx.so cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/test_texture.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/textures/test_texture.png cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/glyph_texture.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/textures/glyph_texture.png cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/aarch64-linux-gnu/libOpenGL.so /usr/lib/aarch64-linux-gnu/libGLX.so /usr/lib/aarch64-linux-gnu/libGLU.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so [ 43%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/contact_overlap.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 43%] Built target ost_gfx make -f modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build.make modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/modules/mol/alg/src/pdbize.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/pdbize.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/gfx/pymod/CMakeFiles/_ost_gfx.dir/wrap_gfx.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/pymod/wrap_gfx.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/mol/alg/src/pdbize.hh:25: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_factory.hh:32, from /build/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.cc:19: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/module_config.hh:23, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/domain_find.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.hh:9, from /build/openstructure-2.3.1/modules/mol/alg/src/adjacency_bitmap.cc:24: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 43%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/pymod/export_scene.cc [ 43%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/similarity_matrix.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:2: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/mol/alg/src/contact_overlap.cc:3: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.hh:7, from /build/openstructure-2.3.1/modules/mol/alg/src/similarity_matrix.cc:1: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/accessibility.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/accessibility.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 43%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/sec_struct.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/sec_struct.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_factory.hh:32, from /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:3: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/nonstandard.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/nonstandard.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:9: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info_group.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/info.hh:32, from /build/openstructure-2.3.1/modules/gfx/pymod/wrap_gfx.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 44%] Building CXX object modules/mol/alg/src/CMakeFiles/ost_mol_alg.dir/molck.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/src/molck.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/modules/gfx/pymod/export_scene.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/accessibility.hh:23, from /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:1: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, from /build/openstructure-2.3.1/modules/mol/alg/src/sec_struct.cc:1: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/bits/stl_algobase.h:64: /usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = float&; _T2 = float&; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp2>::type = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp>::type = float]': /build/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:312:40: required from here /usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 741 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:64: /usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = float; _T2 = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp2>::type = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp>::type = float]': /build/openstructure-2.3.1/modules/mol/alg/src/sec_struct.cc:567:31: required from here /usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 741 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/mol/alg/src/nonstandard.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void ost::mol::alg::CalcContactNodeDegree(const ContactList&)' at /build/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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 file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/mol/alg/src/molck.cc:1: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ 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/openstructure-2.3.1/obj-aarch64-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/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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/openstructure-2.3.1/obj-aarch64-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/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-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/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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/openstructure-2.3.1/obj-aarch64-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/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-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/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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/openstructure-2.3.1/obj-aarch64-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/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/modules/mol/alg/src/molck.cc:4: /build/openstructure-2.3.1/obj-aarch64-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>::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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_base.hh:25, from /build/openstructure-2.3.1/obj-aarch64-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 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /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 file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/find_membrane.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/src/find_membrane.cc:1: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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); | ^~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:11: In member function 'void ost::mol::alg::AdjacencyBitmap::set(size_t, size_t, bool, bool)', inlined from 'ost::mol::alg::AdjacencyBitmap::AdjacencyBitmap(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, int, int)' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:49:16, inlined from 'static ost::mol::alg::DomainsPtr ost::mol::alg::Domains::FromDistMats(const ost::mol::alg::DistanceMatrix&, const ost::mol::alg::DistanceMatrix&, Real, Real, Real, int, bool, bool)' at /build/openstructure-2.3.1/modules/mol/alg/src/domain_find.cc:363:37: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/adjacency_bitmap.hh:109:23: warning: 'malloc' may be used uninitialized [-Wmaybe-uninitialized] 109 | data_[byte_index] &= ~(one << bit_index); | ~~~~~~~~~~~~~~~~^ 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 46%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gfx_obj.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/pymod/export_gfx_obj.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/dft.hh:24, from /build/openstructure-2.3.1/modules/mol/alg/src/entity_to_density.cc:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_entity.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/pymod/export_entity.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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/symmetry_node.hh:22, from /build/openstructure-2.3.1/modules/gfx/pymod/export_symmetry_node.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_surface.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/pymod/export_surface.cc [ 46%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primitives.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/modules/gfx/pymod/export_gfx_obj.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gfx/pymod/export_entity.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/bits/stl_algobase.h:64: /usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = float&; _T2 = float&; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp2>::type = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp>::type = float]': /build/openstructure-2.3.1/modules/gfx/pymod/color_by_def.hh:124:49: required from here /usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 741 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ In file included from /usr/include/c++/12/bits/stl_algobase.h:64: /usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = float&; _T2 = float&; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp2>::type = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp>::type = float]': /build/openstructure-2.3.1/modules/gfx/pymod/color_by_def.hh:124:49: required from here /usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 741 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ [ 46%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_primlist.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/pymod/export_primlist.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/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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/primitives.hh:22, from /build/openstructure-2.3.1/modules/gfx/pymod/export_primitives.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/surface.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/surface.hh:31, from /build/openstructure-2.3.1/modules/gfx/pymod/export_surface.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/bits/stl_algobase.h:64: /usr/include/c++/12/bits/stl_pair.h: In instantiation of 'constexpr std::pair::type>::__type, typename std::__strip_reference_wrapper::type>::__type> std::make_pair(_T1&&, _T2&&) [with _T1 = float&; _T2 = float&; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp2>::type = float; typename __strip_reference_wrapper::type>::__type = float; typename decay<_Tp>::type = float]': /build/openstructure-2.3.1/modules/gfx/pymod/color_by_def.hh:124:49: required from here /usr/include/c++/12/bits/stl_pair.h:741:5: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 741 | make_pair(_T1&& __x, _T2&& __y) | ^~~~~~~~~ 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:778:21: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:778:21: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-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/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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::AtomBase]' at /build/openstructure-2.3.1/obj-aarch64-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/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-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/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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/openstructure-2.3.1/obj-aarch64-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/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:803:35: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/modules/mol/alg/src/accessibility.cc:803:35: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-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/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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/openstructure-2.3.1/obj-aarch64-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/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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); | ^~~~ [ 46%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_scene_observer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/pymod/export_scene_observer.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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/prim_list.hh:28, from /build/openstructure-2.3.1/modules/gfx/pymod/export_primlist.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_render_options.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/pymod/export_render_options.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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-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/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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); | ^~~~ [ 46%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/pymod/export_color.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 46%] Linking CXX shared library ../../../../stage/lib/libost_mol_alg.so cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/atom_scattering_properties.txt /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/atom_scattering_properties.txt cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/stereo_chemical_props.txt /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/stereo_chemical_props.txt cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: /usr/lib/aarch64-linux-gnu/libboost_program_options.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-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/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-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/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libsqlite3.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 46%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src/CMakeFiles/ost_io.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 46%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/io_manager.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/io_manager.cc [ 46%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_gradient.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/pymod/export_gradient.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 46%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_color_ops.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/pymod/export_color_ops.cc [ 46%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_glwin_base.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/pymod/export_glwin_base.cc [ 47%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_exporter.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/pymod/export_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/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( | ^~~~~~~~~~~~~~~~~~~~ /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/openstructure-2.3.1/modules/io/src/io_manager.cc:19: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/pymod/export_color.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ /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/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 /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gradient.hh:28, from /build/openstructure-2.3.1/modules/gfx/pymod/export_gradient.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh:24, from /build/openstructure-2.3.1/modules/gfx/pymod/export_color_ops.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 47%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_bitmap.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/pymod/export_bitmap.cc [ 47%] Building CXX object modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/export_map.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gfx/pymod/export_map.cc [ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/convert.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/convert.cc [ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/io_utils.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/io_utils.cc [ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_crd_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.cc [ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pqr_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.cc [ 47%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/pdb_reader.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/map.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/map_iso.hh:28, from /build/openstructure-2.3.1/modules/gfx/pymod/export_map.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.cc:33: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.cc:35: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.cc:31: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.cc:38: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/pdb_writer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/pdb_writer.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.cc:34: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.cc:35: /build/openstructure-2.3.1/obj-aarch64-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/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 | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_writer.cc:35: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/entity_io_sdf_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.cc [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/sdf_reader.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh:35, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.cc:35: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25: /build/openstructure-2.3.1/obj-aarch64-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%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/gfx/_ost_gfx.so cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/pymod/gradients.xml /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/scene/gradients.xml cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_gfx.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_seq.so.2.3.1 ../../../stage/lib/libost_mol.so.2.3.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libOpenGL.so /usr/lib/aarch64-linux-gnu/libGLX.so /usr/lib/aarch64-linux-gnu/libGLU.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/save_entity.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/sdf_reader.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/load_entity.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/load_entity.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gfx/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gfx/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gfx/pymod/py_gfx_obj.py\",\"/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 48%] Built target _ost_gfx 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 48%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/wrap_mol_alg.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/pymod/wrap_mol_alg.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/openstructure-2.3.1/modules/io/src/mol/save_entity.cc:20: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/load_entity.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/openstructure-2.3.1/modules/io/src/mol/load_entity.cc:24: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh:35, from /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/surface_io_msms_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/format/alt_sstream.hpp:22, from /usr/include/boost/format/internals.hpp:24, from /usr/include/boost/format.hpp:38, from /build/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 48%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/surface.hh:22, from /build/openstructure-2.3.1/modules/io/src/mol/surface_io_handler.hh:25, from /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.hh:22, from /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:23, from /build/openstructure-2.3.1/modules/mol/alg/pymod/wrap_mol_alg.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh: In member function 'std::pair ost::mol::alg::StereoChemicalBondViolation::GetAllowedRange() const': /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh:91:48: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | std::pair GetAllowedRange() const { return allowed_range_; } | ^ [ 50%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/io_profile.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/io_profile.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/load_surface.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 50%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/dcd_io.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/dcd_io.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/openstructure-2.3.1/modules/io/src/mol/load_surface.cc:23: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 50%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/star_parser.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/star_parser.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:30, from /build/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.cc:1: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/chem_class.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/modules/io/src/mol/io_profile.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/io_profile.cc:1: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 50%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.cc [ 50%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/mmcif_info.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.cc:33: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.cc:40: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 50%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/pdb_str.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/pdb_str.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh:25, from /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.cc:21: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/io_exception.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/profile.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25, from /build/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.cc:28: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh:23, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.cc:22: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 50%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.cc [ 50%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/mol/omf.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/mol/omf.cc [ 50%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc [ 50%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/load.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/seq/load.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/stereochemical_params_reader.hh:23, from /build/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh: In member function 'std::pair ost::mol::alg::StereoChemicalBondViolation::GetAllowedRange() const': /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh:91:48: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | std::pair GetAllowedRange() const { return allowed_range_; } | ^ [ 51%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/save.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/seq/save.cc [ 51%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/io/src/seq/load.hh:27, from /build/openstructure-2.3.1/modules/io/src/seq/load.cc:19: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/module_config.hh:22, from /build/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 /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/modules/io/src/mol/omf.cc:2: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/atom_handle.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mmcif_info.hh:25, from /build/openstructure-2.3.1/modules/io/src/mol/omf.hh:29, from /build/openstructure-2.3.1/modules/io/src/mol/omf.cc:6: /build/openstructure-2.3.1/obj-aarch64-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/seq/pir_io_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.hh:25, from /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.cc:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/openstructure-2.3.1/modules/io/src/seq/save.cc:22: /build/openstructure-2.3.1/obj-aarch64-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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.hh:25, from /build/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.cc:19: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/module_config.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh:25, from /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.cc:19: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/module_config.hh:22, from /build/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 | ^~~~~~~~ [ 51%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/hhm_io_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/seq/hhm_io_handler.cc [ 51%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/seq/pssm_io_handler.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.hh:26, from /build/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.cc:22: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/map.hh:22, from /build/openstructure-2.3.1/modules/io/src/img/load_map.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_spi_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/openstructure-2.3.1/modules/io/src/img/load_map.cc:24: /build/openstructure-2.3.1/obj-aarch64-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_situs_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.cc [ 51%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.cc [ 52%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.cc:37: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 52%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.cc:35: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 52%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.cc In file included from /usr/include/boost/bind.hpp:30, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.cc:34: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.cc:37: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:34: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.cc:43: /build/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/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:24: /usr/include/aarch64-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/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/aarch64-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/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/aarch64-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.cc:76: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/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/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/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/aarch64-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/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/aarch64-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/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/aarch64-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/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/aarch64-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/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/aarch64-linux-gnu/tiff.h:80:37: note: declared here 80 | typedef TIFF_MSC_DEPRECATED uint8_t uint8 TIFF_GCC_DEPRECATED; | ^~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/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/aarch64-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/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/aarch64-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/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/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/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/aarch64-linux-gnu/tiff.h:80:37: note: declared here 80 | typedef TIFF_MSC_DEPRECATED uint8_t uint8 TIFF_GCC_DEPRECATED; | ^~~~~ /build/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/aarch64-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/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/aarch64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 52%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.cc [ 52%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc [ 52%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.cc [ 52%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.cc:31: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 52%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/map_io_df3_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/alg_transform.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/transform.hh:24, from /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 52%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/image_format.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/img/image_format.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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.cc:38: /build/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/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:24: /usr/include/aarch64-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/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/aarch64-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/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/aarch64-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ /build/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/aarch64-linux-gnu/tiff.h:86:38: note: declared here 86 | typedef TIFF_MSC_DEPRECATED uint32_t uint32 TIFF_GCC_DEPRECATED; | ^~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.cc:34: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 52%] Building CXX object modules/io/src/CMakeFiles/ost_io.dir/img/tiff_util.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/src/img/tiff_util.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.cc:34: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.cc:34: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 52%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_svd_superpose.cc.o [ 52%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_clash.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/pymod/export_clash.cc cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/pymod/export_svd_superpose.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/normalizer_factory.hh:27, from /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:27, from /build/openstructure-2.3.1/modules/io/src/img/tiff_util.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/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/openstructure-2.3.1/modules/io/src/img/tiff_util.hh:24: /usr/include/aarch64-linux-gnu/tiff.h:85:37: note: declared here 85 | typedef TIFF_MSC_DEPRECATED int32_t int32 TIFF_GCC_DEPRECATED; | ^~~~~ /build/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/aarch64-linux-gnu/tiff.h:82:37: note: declared here 82 | typedef TIFF_MSC_DEPRECATED int16_t int16 TIFF_GCC_DEPRECATED; | ^~~~~ /build/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/aarch64-linux-gnu/tiff.h:79:36: note: declared here 79 | typedef TIFF_MSC_DEPRECATED int8_t int8 TIFF_GCC_DEPRECATED; | ^~~~ /build/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/aarch64-linux-gnu/tiff.h:83:38: note: declared here 83 | typedef TIFF_MSC_DEPRECATED uint16_t uint16 TIFF_GCC_DEPRECATED; | ^~~~~~ [ 52%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_trajectory_analysis.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/pymod/export_trajectory_analysis.cc [ 52%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_structure_analysis.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/pymod/export_structure_analysis.cc [ 52%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_accessibility.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/pymod/export_accessibility.cc [ 52%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_contact_overlap.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/pymod/export_contact_overlap.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/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 /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_svd_superpose.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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 /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/clash_score.hh:26, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_clash.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 53%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_sec_structure.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/pymod/export_sec_structure.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/trajectory_analysis.hh:29, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_trajectory_analysis.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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 /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/structure_analysis.hh:28, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_structure_analysis.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 53%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_non_standard.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/pymod/export_non_standard.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/accessibility.hh:23, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_accessibility.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/contact_overlap.hh:6, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_contact_overlap.cc:4: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/contact_overlap.hh:8: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 53%] Linking CXX shared library ../../../stage/lib/libost_io.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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 CMakeFiles/ost_io.dir/mol/entity_io_mae_handler.cc.o CMakeFiles/ost_io.dir/mol/pdb_reader.cc.o CMakeFiles/ost_io.dir/mol/entity_io_pdb_handler.cc.o CMakeFiles/ost_io.dir/mol/pdb_writer.cc.o CMakeFiles/ost_io.dir/mol/entity_io_sdf_handler.cc.o CMakeFiles/ost_io.dir/mol/entity_io_mmcif_handler.cc.o CMakeFiles/ost_io.dir/mol/sdf_reader.cc.o CMakeFiles/ost_io.dir/mol/sdf_writer.cc.o CMakeFiles/ost_io.dir/mol/save_entity.cc.o CMakeFiles/ost_io.dir/mol/load_entity.cc.o CMakeFiles/ost_io.dir/mol/surface_io_msms_handler.cc.o CMakeFiles/ost_io.dir/mol/load_surface.cc.o CMakeFiles/ost_io.dir/mol/chemdict_parser.cc.o CMakeFiles/ost_io.dir/mol/io_profile.cc.o CMakeFiles/ost_io.dir/mol/dcd_io.cc.o CMakeFiles/ost_io.dir/mol/star_parser.cc.o CMakeFiles/ost_io.dir/mol/mmcif_reader.cc.o CMakeFiles/ost_io.dir/mol/mmcif_info.cc.o CMakeFiles/ost_io.dir/mol/pdb_str.cc.o CMakeFiles/ost_io.dir/mol/stereochemical_params_reader.cc.o CMakeFiles/ost_io.dir/mol/omf.cc.o CMakeFiles/ost_io.dir/seq/clustal_io_handler.cc.o CMakeFiles/ost_io.dir/seq/load.cc.o CMakeFiles/ost_io.dir/seq/save.cc.o CMakeFiles/ost_io.dir/seq/fasta_io_handler.cc.o CMakeFiles/ost_io.dir/seq/pir_io_handler.cc.o CMakeFiles/ost_io.dir/seq/promod_io_handler.cc.o CMakeFiles/ost_io.dir/seq/hhm_io_handler.cc.o CMakeFiles/ost_io.dir/seq/pssm_io_handler.cc.o CMakeFiles/ost_io.dir/img/load_map.cc.o CMakeFiles/ost_io.dir/img/map_io_dx_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_spi_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_situs_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_mrc_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_dm3_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_tiff_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_dat_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_ipl_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_jpk_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_nanoscope_handler.cc.o CMakeFiles/ost_io.dir/img/map_io_png_handler.cc.o 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_mol_alg.so.2.3.1 ../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so ../../../stage/lib/libost_conop.so.2.3.1 ../../../stage/lib/libost_db.so.2.3.1 /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img.so.2.3.1 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 53%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src/CMakeFiles/chemdict_tool.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 53%] Building CXX object modules/conop/src/CMakeFiles/chemdict_tool.dir/chemdict_tool.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/conop/src/chemdict_tool.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 53%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_molck.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_sec_structure.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 53%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_membrane.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/pymod/export_membrane.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_non_standard.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 53%] Building CXX object modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/export_entity_to_density.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/mol/alg/pymod/export_entity_to_density.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/compound_lib_base.hh:5, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/compound_lib.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh:30, from /build/openstructure-2.3.1/modules/conop/src/chemdict_tool.cc:32: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/gui/src/CMakeFiles/ost_gui.dir/build.make modules/gui/src/CMakeFiles/ost_gui.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 53%] Generating tools/moc_tool_options_win.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp_parameters [ 53%] Generating data_viewer/moc_argand.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp_parameters [ 53%] Generating data_viewer/moc_data_viewer.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp_parameters [ 53%] Generating data_viewer/moc_data_viewer_panel_base.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp_parameters [ 55%] Generating data_viewer/moc_fft_panel.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp_parameters [ 55%] Generating data_viewer/moc_info_panel.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp_parameters [ 55%] Generating data_viewer/moc_null_overlay.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_null_overlay.cpp_parameters [ 55%] Generating data_viewer/moc_overlay_base.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_base.cpp_parameters [ 55%] Generating data_viewer/moc_overlay_manager_gui.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_manager_gui.cpp_parameters [ 55%] Generating data_viewer/moc_pointlist_overlay_base.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp_parameters [ 55%] Generating messages/moc_log_reader.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/messages && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/messages/moc_log_reader.cpp_parameters [ 55%] Generating messages/moc_message_box_widget.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/messages && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/messages/moc_message_box_widget.cpp_parameters [ 55%] Generating messages/moc_message_widget.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/messages && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/messages/moc_message_widget.cpp_parameters [ 55%] Generating moc_dock_widget.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_dock_widget.cpp_parameters [ 55%] Generating moc_file_browser.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_file_browser.cpp_parameters [ 55%] Generating moc_file_type_dialog.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp_parameters [ 55%] Generating moc_file_viewer.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_file_viewer.cpp_parameters [ 55%] Generating moc_gl_canvas.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_gl_canvas.cpp_parameters [ 56%] Generating moc_gl_win.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_gl_win.cpp_parameters [ 56%] Generating moc_gosty_app.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_gosty_app.cpp_parameters [ 56%] Generating moc_main.cpp make -f modules/io/tests/CMakeFiles/test_mae_standalone.dir/build.make modules/io/tests/CMakeFiles/test_mae_standalone.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_main.cpp_parameters make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/tests/CMakeFiles/test_mae_standalone.dir/DependInfo.cmake --color= [ 56%] Generating moc_main_area.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_main_area.cpp_parameters make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 56%] Building CXX object modules/io/tests/CMakeFiles/test_mae_standalone.dir/test_mae_standalone.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/io/tests/test_mae_standalone.cc [ 56%] Generating moc_main_window.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_main_window.cpp_parameters [ 56%] Generating moc_perspective.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_perspective.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/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( | ^~~~~~~~~~~~~~~~~~~~ [ 56%] Generating moc_scene_menu.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_scene_menu.cpp_parameters /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 56%] Generating moc_scene_selection.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_scene_selection.cpp_parameters [ 56%] Generating moc_widget.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_widget.cpp_parameters [ 56%] Generating moc_widget_geom_handler.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_widget_geom_handler.cpp_parameters [ 57%] Generating moc_widget_pool.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_widget_pool.cpp_parameters [ 57%] Generating panels/moc_bottom_bar.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_bottom_bar.cpp_parameters [ 57%] Generating panels/moc_button_bar.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_button_bar.cpp_parameters [ 57%] Generating panels/moc_button_box.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_button_box.cpp_parameters [ 57%] Generating panels/moc_drop_box.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp_parameters [ 57%] Generating panels/moc_event_button.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_event_button.cpp_parameters [ 57%] Generating panels/moc_panel_bar.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_panel_bar.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 57%] Generating panels/moc_panel_bar_widget_holder.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_panel_bar_widget_holder.cpp_parameters [ 58%] Generating panels/moc_panel_manager.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_panel_manager.cpp_parameters [ 58%] Generating panels/moc_panel_widget_container.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_panel_widget_container.cpp_parameters In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/molck.hh:23, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_molck.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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%] Generating panels/moc_side_bar.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_side_bar.cpp_parameters [ 58%] Generating panels/moc_splitter_panel_bar.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_splitter_panel_bar.cpp_parameters [ 58%] Generating panels/moc_tabbed_panel_bar.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_tabbed_panel_bar.cpp_parameters [ 58%] Generating python_shell/moc_completer_base.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_completer_base.cpp_parameters [ 58%] Generating python_shell/moc_gutter.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_gutter.cpp_parameters [ 58%] Generating python_shell/moc_main_thread_runner.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_main_thread_runner.cpp_parameters [ 58%] Generating python_shell/moc_output_redirector.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_output_redirector.cpp_parameters [ 58%] Generating python_shell/moc_path_completer.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_path_completer.cpp_parameters [ 58%] Generating python_shell/moc_python_completer.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_completer.cpp_parameters [ 58%] Generating python_shell/moc_python_interpreter.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_interpreter.cpp_parameters [ 58%] Generating python_shell/moc_python_interpreter_worker.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_namespace_tree_model.cpp_parameters [ 60%] Generating python_shell/moc_python_shell.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_shell.cpp_parameters [ 60%] Generating python_shell/moc_python_shell_widget.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_shell_widget.cpp_parameters [ 60%] Generating python_shell/moc_state.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_state.cpp_parameters [ 60%] Generating python_shell/moc_state_machine.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_state_machine.cpp_parameters [ 60%] Generating python_shell/moc_text_logger.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp_parameters [ 60%] Generating python_shell/moc_transition.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_transition.cpp_parameters [ 60%] Generating python_shell/moc_transition_guard.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_transition_guard.cpp_parameters [ 60%] Generating scene_win/moc_context_menu.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp_parameters [ 60%] Generating scene_win/moc_current_selection_node.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp_parameters In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/find_membrane.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_membrane.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 61%] Generating scene_win/moc_custom_part_node.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 61%] Generating scene_win/moc_entity_node.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp_parameters [ 61%] Generating scene_win/moc_entity_part_node.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp_parameters [ 61%] Generating scene_win/moc_gfx_scene_node.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_gfx_scene_node.cpp_parameters [ 61%] Generating scene_win/moc_label_node.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_label_node.cpp_parameters [ 61%] Generating scene_win/moc_render_mode_node.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp_parameters In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/modules/io/tests/test_mae_standalone.cc:2: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 61%] Generating scene_win/moc_render_modes_node.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp_parameters In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/entity_to_density.hh:4, from /build/openstructure-2.3.1/modules/mol/alg/pymod/export_entity_to_density.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 61%] Generating scene_win/moc_root_node.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_root_node.cpp_parameters [ 61%] Generating scene_win/moc_scene_node.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_node.cpp_parameters [ 61%] Generating scene_win/moc_scene_win.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp_parameters [ 61%] Generating scene_win/moc_scene_win_model.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp_parameters [ 61%] Linking CXX executable ../../../stage/bin/chemdict_tool cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so [ 61%] Generating sequence_viewer/moc_align_properties_painter.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp_parameters make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 61%] Built target chemdict_tool make -f modules/mol/alg/src/CMakeFiles/lddt.dir/build.make modules/mol/alg/src/CMakeFiles/lddt.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src/CMakeFiles/lddt.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 61%] Building CXX object modules/mol/alg/src/CMakeFiles/lddt.dir/lddt.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/alg/src/lddt.cc [ 61%] Generating sequence_viewer/moc_alignment_view_object.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp_parameters [ 61%] Generating sequence_viewer/moc_background_painter.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp_parameters [ 61%] Linking CXX executable ../../../stage/bin/test_mae_standalone cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/aarch64-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/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so [ 61%] Generating sequence_viewer/moc_base_row.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp_parameters [ 62%] Generating sequence_viewer/moc_base_view_object.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp_parameters make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 62%] Built target test_mae_standalone make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 62%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/forcefield.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/src/CMakeFiles/ost_mol_mm.dir/forcefield.cc.o -MF CMakeFiles/ost_mol_mm.dir/forcefield.cc.o.d -o CMakeFiles/ost_mol_mm.dir/forcefield.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/forcefield.cc [ 62%] Generating sequence_viewer/moc_conservation_painter.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp_parameters [ 62%] Generating sequence_viewer/moc_painter.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp_parameters [ 62%] Generating sequence_viewer/moc_secstr_row.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp_parameters [ 62%] Generating sequence_viewer/moc_seq_secstr_painter.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp_parameters [ 64%] Generating sequence_viewer/moc_seq_selection_painter.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp_parameters [ 64%] Generating sequence_viewer/moc_seq_text_painter.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp_parameters [ 64%] Generating sequence_viewer/moc_sequence_delegate.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp_parameters [ 64%] Generating sequence_viewer/moc_sequence_model.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp_parameters [ 64%] Generating sequence_viewer/moc_sequence_row.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp_parameters [ 64%] Generating sequence_viewer/moc_sequence_search_bar.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp_parameters [ 64%] Generating sequence_viewer/moc_sequence_table_view.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp_parameters [ 64%] Generating sequence_viewer/moc_sequence_view_object.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp_parameters [ 64%] Generating sequence_viewer/moc_sequence_viewer.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp_parameters [ 64%] Generating sequence_viewer/moc_tick_painter.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp_parameters [ 64%] Generating sequence_viewer/moc_title_row.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp_parameters [ 64%] Generating tools/moc_measure_tool.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp_parameters [ 65%] Generating tools/moc_tool.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool.cpp_parameters [ 65%] Generating tools/moc_tool_bar.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_bar.cpp_parameters [ 65%] Generating tools/moc_tool_manager.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_manager.cpp_parameters [ 65%] Generating tools/moc_tool_option.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_option.cpp_parameters [ 65%] Generating tools/moc_tool_option_group.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_option_group.cpp_parameters [ 65%] Generating tools/moc_tool_options.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_options.cpp_parameters [ 65%] Generating tools/moc_tool_options_widget.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_options_widget.cpp_parameters [ 65%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/src/CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o -MF CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o.d -o CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/ff_reader.cc [ 65%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/src/CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o -MF CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o.d -o CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/buildingblock.cc [ 65%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/src/CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o -MF CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o.d -o CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/gromacs_block_modifiers.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_file_browser.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:30: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, from /build/openstructure-2.3.1/modules/mol/mm/src/forcefield.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:24, from /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:31: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh: In member function 'std::pair ost::mol::alg::StereoChemicalBondViolation::GetAllowedRange() const': /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh:91:48: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | std::pair GetAllowedRange() const { return allowed_range_; } | ^ [ 65%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/src/CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o -MF CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o.d -o CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/heuristic_block_modifiers.cc In file included from /build/openstructure-2.3.1/modules/mol/alg/src/lddt.cc:39: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/amino_acids.hh: At global scope: /build/openstructure-2.3.1/obj-aarch64-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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/gromacs_block_modifiers.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /build/openstructure-2.3.1/modules/mol/mm/src/buildingblock.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/file_browser.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_file_browser.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:32, from /build/openstructure-2.3.1/modules/mol/mm/src/ff_reader.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/heuristic_block_modifiers.hh:28, from /build/openstructure-2.3.1/modules/mol/mm/src/heuristic_block_modifiers.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/heuristic_block_modifiers.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/mol/alg/_ost_mol_alg.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-linux-gnu/libboost_atomic.so ../../../../stage/lib/libost_img_alg.so.2.3.1 ../../../../stage/lib/libost_img.so.2.3.1 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-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/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libsqlite3.so [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/alg/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/alg/pymod/views.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./views.pyc\",\"views.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/alg/pymod/superpose.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./superpose.pyc\",\"superpose.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/alg/pymod/qsscoring.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./qsscoring.pyc\",\"qsscoring.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/alg/pymod/trajectory_analysis.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./trajectory_analysis.pyc\",\"trajectory_analysis.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/alg/pymod/structure_analysis.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./structure_analysis.pyc\",\"structure_analysis.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/alg/pymod/helix_kinks.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./helix_kinks.pyc\",\"helix_kinks.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/alg/pymod/hbond.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/alg/./hbond.pyc\",\"hbond.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 65%] Built target _ost_mol_alg make -f tools/molck/CMakeFiles/molck.dir/build.make tools/molck/CMakeFiles/molck.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/tools/molck /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/tools/molck /build/openstructure-2.3.1/obj-aarch64-linux-gnu/tools/molck/CMakeFiles/molck.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f tools/molck/CMakeFiles/molck.dir/build.make tools/molck/CMakeFiles/molck.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 65%] Building CXX object tools/molck/CMakeFiles/molck.dir/main.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/tools/molck && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/tools/molck/main.cc [ 65%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/interaction.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/src/CMakeFiles/ost_mol_mm.dir/interaction.cc.o -MF CMakeFiles/ost_mol_mm.dir/interaction.cc.o.d -o CMakeFiles/ost_mol_mm.dir/interaction.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/interaction.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/file_type_dialog.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_file_type_dialog.cpp:10: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/modules/mol/mm/src/interaction.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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%] Linking CXX executable ../../../../stage/bin/lddt cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_program_options.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-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/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so [ 65%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/simulation.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/src/CMakeFiles/ost_mol_mm.dir/simulation.cc.o -MF CMakeFiles/ost_mol_mm.dir/simulation.cc.o.d -o CMakeFiles/ost_mol_mm.dir/simulation.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/simulation.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/conop.hh:24, from /build/openstructure-2.3.1/tools/molck/main.cc:8: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 65%] Built target lddt make -f modules/io/pymod/CMakeFiles/_ost_io.dir/build.make modules/io/pymod/CMakeFiles/_ost_io.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/pymod/CMakeFiles/_ost_io.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 65%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/wrap_io.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/pymod/wrap_io.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/tools/molck/main.cc:10: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 65%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/modeller.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/src/CMakeFiles/ost_mol_mm.dir/modeller.cc.o -MF CMakeFiles/ost_mol_mm.dir/modeller.cc.o.d -o CMakeFiles/ost_mol_mm.dir/modeller.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/modeller.cc [ 65%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/src/CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o -MF CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o.d -o CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/state_extractor.cc [ 65%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_file_viewer.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:26, from /build/openstructure-2.3.1/modules/mol/mm/src/simulation.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/modules/mol/mm/src/modeller.cc:20: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:27: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 65%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/observer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/src/CMakeFiles/ost_mol_mm.dir/observer.cc.o -MF CMakeFiles/ost_mol_mm.dir/observer.cc.o.d -o CMakeFiles/ost_mol_mm.dir/observer.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/observer.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 66%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_gl_canvas.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/openstructure-2.3.1/modules/io/pymod/wrap_io.cc:23: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/system_creator.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/src/CMakeFiles/ost_mol_mm.dir/system_creator.cc.o -MF CMakeFiles/ost_mol_mm.dir/system_creator.cc.o.d -o CMakeFiles/ost_mol_mm.dir/system_creator.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/system_creator.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/stereochemical_params_reader.hh:23, from /build/openstructure-2.3.1/modules/io/pymod/wrap_io.cc:36: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh: In member function 'std::pair ost::mol::alg::StereoChemicalBondViolation::GetAllowedRange() const': /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh:91:48: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | std::pair GetAllowedRange() const { return allowed_range_; } | ^ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/observer.hh:26, from /build/openstructure-2.3.1/modules/mol/mm/src/observer.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/observer.hh:24: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/gl_canvas.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_gl_canvas.cpp:10: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/observer.hh:33: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_gl_win.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:28, from /build/openstructure-2.3.1/modules/mol/mm/src/system_creator.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Linking CXX executable ../../stage/bin/molck cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../stage/lib/libost_io.so.2.3.1 ../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_program_options.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 67%] Built target molck [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_scene_menu.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 67%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/src/CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o -MF CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o.d -o CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_gosty_app.cpp [ 67%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/topology.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/src/CMakeFiles/ost_mol_mm.dir/topology.cc.o -MF CMakeFiles/ost_mol_mm.dir/topology.cc.o.d -o CMakeFiles/ost_mol_mm.dir/topology.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/topology.cc [ 67%] Building CXX object modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/steep.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/c++ -DOST_MODULE_OST_MOL_MM -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -Dost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/src/CMakeFiles/ost_mol_mm.dir/steep.cc.o -MF CMakeFiles/ost_mol_mm.dir/steep.cc.o.d -o CMakeFiles/ost_mol_mm.dir/steep.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/src/steep.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:29, from /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology.hh:31, from /build/openstructure-2.3.1/modules/mol/mm/src/topology.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology.hh:23: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_main.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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/gosty_app.hh:28, from /build/openstructure-2.3.1/obj-aarch64-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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_area.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_main_area.cpp [ 67%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_pdb_io.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_perspective.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_perspective.cpp [ 67%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_mmcif_io.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_dock_widget.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_dock_widget.cpp [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_main_window.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_main_window.cpp [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_scene_selection.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_scene_selection.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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_dock_widget.cpp:10: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qdockwidget.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QDockWidget:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/dock_widget.hh:31: /usr/include/aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, from /build/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 67%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_widget.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/io/pymod/export_pdb_io.cc:23: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_main_window.cpp:10: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QMainWindow:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main_window.hh:35: /usr/include/aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/scene_selection.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_scene_selection.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/widget_state_saver.hh: In instantiation of 'ost::gui::WidgetStateSaver::~WidgetStateSaver() [with BASE = QMainWindow]': /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/../../../../modules/gui/src/main.hh:40:25: required from here /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~~~~~~~~~~~~~~~ /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_widget_geom_handler.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_widget_geom_handler.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/moc_widget_pool.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_widget_pool.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, from /build/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25, from /build/openstructure-2.3.1/modules/io/pymod/export_mmcif_io.cc:27: /build/openstructure-2.3.1/obj-aarch64-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/c++/12/string:53, from /usr/include/c++/12/stdexcept:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:28: 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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)' at /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:136:29: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In static member function 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/12/string: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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)' at /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:136:29: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In static member function 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)' at /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:136:29: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In static member function 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)' at /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:136:29: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In static member function 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)' at /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:137:29: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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 static member function 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)' at /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:137:29: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In static member function 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)' at /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:137:29: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In static member function 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)': /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 = bool; 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 = bool; 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 = bool; 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::SetBoolProp(const String&, bool) [with H = ost::mol::ResidueBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:372:38, inlined from 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)' at /build/openstructure-2.3.1/modules/mol/mm/src/topology_creator.cc:137:29: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In static member function 'static ost::mol::mm::TopologyPtr ost::mol::mm::TopologyCreator::Create(ost::mol::EntityHandle&, ost::mol::mm::SettingsPtr)': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_widget.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/messages/moc_message_widget.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_message_box_widget.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/messages/moc_message_box_widget.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/moc_log_reader.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/messages/moc_log_reader.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_align_properties_painter.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_background_painter.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp [ 69%] Linking CXX shared library ../../../../stage/lib/libost_mol_mm.so cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/AMBER03.dat /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/forcefields/AMBER03.dat cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/CHARMM27.dat /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/forcefields/CHARMM27.dat cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_mm.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-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_mm.so.2.3 -o ../../../../stage/lib/libost_mol_mm.so.2.3.1 CMakeFiles/ost_mol_mm.dir/forcefield.cc.o CMakeFiles/ost_mol_mm.dir/ff_reader.cc.o CMakeFiles/ost_mol_mm.dir/buildingblock.cc.o CMakeFiles/ost_mol_mm.dir/gromacs_block_modifiers.cc.o CMakeFiles/ost_mol_mm.dir/heuristic_block_modifiers.cc.o CMakeFiles/ost_mol_mm.dir/interaction.cc.o CMakeFiles/ost_mol_mm.dir/simulation.cc.o CMakeFiles/ost_mol_mm.dir/modeller.cc.o CMakeFiles/ost_mol_mm.dir/state_extractor.cc.o CMakeFiles/ost_mol_mm.dir/observer.cc.o CMakeFiles/ost_mol_mm.dir/system_creator.cc.o CMakeFiles/ost_mol_mm.dir/topology_creator.cc.o CMakeFiles/ost_mol_mm.dir/topology.cc.o CMakeFiles/ost_mol_mm.dir/steep.cc.o -L/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: /usr/lib/aarch64-linux-gnu/libboost_program_options.so ../../../../stage/lib/libost_io.so.2.3.1 /usr/lib/aarch64-linux-gnu/libOpenMM.so ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_program_options.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 /usr/lib/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_base_row.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_conservation_painter.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_painter.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/align_properties_painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_align_properties_painter.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E cmake_symlink_library ../../../../stage/lib/libost_mol_mm.so.2.3.1 ../../../../stage/lib/libost_mol_mm.so.2.3 ../../../../stage/lib/libost_mol_mm.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 69%] Built target ost_mol_mm [ 69%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_secstr_row.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/background_painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_background_painter.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_row.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/secstr_row.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_secstr_row.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/conservation_painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_conservation_painter.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_painter.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_secstr_painter.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp [ 70%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_selection_painter.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp [ 71%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_omf_io.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/pymod/export_omf_io.cc [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_seq_text_painter.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_delegate.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_model.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_secstr_painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_secstr_painter.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_row.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_selection_painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_selection_painter.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/seq_text_painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_seq_text_painter.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_delegate.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_model.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_row.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_row.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_search_bar.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/omf.hh:26, from /build/openstructure-2.3.1/modules/io/pymod/export_omf_io.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mmcif_info.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/omf.hh:29: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_table_view.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_sequence_viewer.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_search_bar.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_search_bar.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 71%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/moc_tick_painter.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_table_view.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_table_view.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_title_row.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/openstructure-2.3.1/obj-aarch64-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_alignment_view_object.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_viewer.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_viewer.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/tick_painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_tick_painter.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/title_row.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_title_row.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_base_view_object.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp [ 73%] Building CXX object modules/io/pymod/CMakeFiles/_ost_io.dir/export_map_io.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/io/pymod/export_map_io.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/alignment_view_object.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_alignment_view_object.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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_view_object.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_main_thread_runner.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_row.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/base_view_object.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_base_view_object.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_completer_base.cpp [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_gutter.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_gutter.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 73%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_output_redirector.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_output_redirector.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/moc_sequence_view_object.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_path_completer.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_path_completer.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/map.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh:26, from /build/openstructure-2.3.1/modules/io/pymod/export_map_io.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_python_completer.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_python_completer.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/sequence_viewer/../../../../../modules/gui/src/sequence_viewer/sequence_view_object.hh:32: /build/openstructure-2.3.1/obj-aarch64-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/python_shell/moc_python_interpreter.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_text_logger.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state_machine.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_state_machine.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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_state.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_state.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/moc_transition.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/moc_transition_guard.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_shell_widget.hh:28, from /build/openstructure-2.3.1/obj-aarch64-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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_button_bar.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_button_bar.cpp [ 74%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_drop_box.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_drop_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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-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( | ^~~~~~~~~~~~~~~~~~~~ /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_panel_bar.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_panel_bar.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_manager.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_panel_manager.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/../../../../../modules/gui/src/panels/drop_box.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_drop_box.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_bottom_bar.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/transition_guard.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/python_shell/../../../../../modules/gui/src/python_shell/transition.hh:23, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_button_box.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_event_button.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_event_button.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_widget_container.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_panel_widget_container.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_panel_bar_widget_holder.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_panel_bar_widget_holder.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_side_bar.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_side_bar.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_splitter_panel_bar.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_splitter_panel_bar.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/moc_tabbed_panel_bar.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/panels/moc_tabbed_panel_bar.cpp [ 75%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_context_menu.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_current_selection_node.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_custom_part_node.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_gfx_scene_node.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_gfx_scene_node.cpp [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_label_node.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_label_node.cpp [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_node.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_entity_part_node.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/context_menu.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_context_menu.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/current_selection_node.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_current_selection_node.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/custom_part_node.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_custom_part_node.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_mode_node.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_render_modes_node.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/entity_node.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_entity_node.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/entity_part_node.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_entity_part_node.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_root_node.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_root_node.cpp [ 76%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_node.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_node.cpp [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/moc_scene_win.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_mode_node.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_render_mode_node.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_mode_node.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/render_modes_node.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_render_modes_node.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_model.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool.cpp [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option_group.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_option_group.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/scene_win.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_win.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_options.cpp [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_bar.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_bar.cpp [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_option.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_option.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/../../../../../modules/gui/src/scene_win/scene_win_model.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/scene_win/moc_scene_win_model.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool.cpp:10: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/aarch64-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, | ^~~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_manager.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_manager.cpp [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_widget.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_options_widget.cpp [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_measure_tool.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/tool_bar.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_bar.cpp:10: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/aarch64-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, | ^~~~~~~~~ [ 78%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/moc_tool_options_win.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_argand.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_fft_panel.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/tool_manager.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_manager.cpp:10: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/tool_options_win.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_tool_options_win.cpp:10: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/measure_tool.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/moc_measure_tool.cpp:10: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/aarch64-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/argand.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_argand.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : 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/data_viewer/moc_overlay_manager_gui.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_manager_gui.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/info_panel.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_info_panel.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data_observer.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/fft_panel.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_fft_panel.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/tools/../../../../../modules/gui/src/tools/measure_tool.hh:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : 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/data_viewer/moc_data_viewer_panel_base.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : 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/data_viewer/moc_null_overlay.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_null_overlay.cpp [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_overlay_base.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_overlay_base.cpp [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/moc_pointlist_overlay_base.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp [ 79%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/thin_splitter.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/thin_splitter.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_data_viewer_panel_base.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : 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/perspective.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/perspective.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/data_viewer.hh:37: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QMainWindow:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main_window.hh:35: /usr/include/aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/../../../../../modules/gui/src/data_viewer/pointlist_overlay_base.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/data_viewer/moc_pointlist_overlay_base.cpp:10: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_registry.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/widget_registry.cc [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_browser.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/file_browser.cc [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_type_dialog.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/file_type_dialog.cc [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_viewer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/file_viewer.cc [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/main.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/file_browser.hh:23, from /build/openstructure-2.3.1/modules/gui/src/perspective.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/platform.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_canvas.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/gl_canvas.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/modules/gui/src/file_type_dialog.hh:31, from /build/openstructure-2.3.1/modules/gui/src/file_type_dialog.cc:19: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/dock_widget.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/dock_widget.cc [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/main_window.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/main_window.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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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 /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/gl_win.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/gl_win.cc In file included from /build/openstructure-2.3.1/modules/gui/src/dock_widget.cc:25: /build/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/aarch64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qdockwidget.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QDockWidget:1, from /build/openstructure-2.3.1/modules/gui/src/dock_widget.hh:31: /usr/include/aarch64-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/openstructure-2.3.1/modules/gui/src/main_window.cc:25: /build/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/aarch64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QMainWindow:1, from /build/openstructure-2.3.1/modules/gui/src/main_window.hh:35: /usr/include/aarch64-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/openstructure-2.3.1/modules/gui/src/main_window.cc:26: /build/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/aarch64-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/openstructure-2.3.1/modules/gui/src/dock_widget.hh: In member function 'void ost::gui::MainWindow::AddDockWidget(QWidget*, const QString&, bool, int)': /build/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/aarch64-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/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/aarch64-linux-gnu/qt5/QtWidgets/qaction.h:47, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qmenu.h:47, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QMenu:1, from /build/openstructure-2.3.1/modules/gui/src/main_window.hh:36: /usr/include/aarch64-linux-gnu/qt5/QtCore/qvariant.h:530:17: note: declared here 530 | inline QVariant qVariantFromValue(const T &t) | ^~~~~~~~~~~~~~~~~ [ 80%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_menu.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/scene_menu.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/gl_canvas.hh:23, from /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:22: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/file_loader.hh:24, from /build/openstructure-2.3.1/modules/gui/src/main.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/file_loader.hh:30, from /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:34: /build/openstructure-2.3.1/obj-aarch64-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/widget.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/widget.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/file_loader.hh:30: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/modules/gui/src/file_browser.cc: In constructor 'ost::gui::FileBrowser::FileBrowser(QWidget*)': /build/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/aarch64-linux-gnu/qt5/QtWidgets/QDirModel:1, from /build/openstructure-2.3.1/modules/gui/src/file_browser.cc:53: /usr/include/aarch64-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/openstructure-2.3.1/modules/gui/src/file_browser.cc: In constructor 'ost::gui::FileBrowser::FileBrowser(const QString&, QWidget*)': /build/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/aarch64-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); | ^~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/glwin_base.hh:28, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.hh:27, from /build/openstructure-2.3.1/modules/gui/src/main.cc:31: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/aarch64-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, | ^~~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/admin.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/admin.cc /build/openstructure-2.3.1/modules/gui/src/main.cc: In static member function 'static QSize ost::gui::GostyMainWindow::GetDefaultSize()': /build/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/aarch64-linux-gnu/qt5/QtWidgets/QDesktopWidget:1, from /build/openstructure-2.3.1/modules/gui/src/main.cc:35: /usr/include/aarch64-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; | ^~~~~~~~~~~~~~~~~ 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:28, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh: In instantiation of 'ost::gui::WidgetStateSaver::~WidgetStateSaver() [with BASE = QMainWindow]': /build/openstructure-2.3.1/modules/gui/src/main.cc:69:69: required from here /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:263:7: note: 'ost::gui::WidgetStateSaver::' declared here 263 | class WidgetStateSaver: public BASE | ^~~~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh: In instantiation of 'void ost::gui::WidgetStateSaver::set_state_() [with BASE = QMainWindow]': /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/modules/gui/src/main.cc:69:69: required from here /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/widget_state_saver.hh:263:7: note: 'ost::gui::WidgetStateSaver::' declared here 263 | class WidgetStateSaver: public BASE | ^~~~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/gl_canvas.cc: In member function 'void ost::gui::GLCanvas::HandleMouseMoveEvent(QMouseEvent*)': /build/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/aarch64-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/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/aarch64-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/openstructure-2.3.1/modules/gui/src/gl_canvas.cc: In member function 'virtual void ost::gui::GLCanvas::wheelEvent(QWheelEvent*)': /build/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/aarch64-linux-gnu/qt5/QtGui/QMouseEvent:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:25: /usr/include/aarch64-linux-gnu/qt5/QtGui/qevent.h:219:16: note: declared here 219 | inline int delta() const { return qt4D; } | ^~~~~ 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_pool.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/widget_pool.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_widget.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/message_box_widget.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/messages/log_reader.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/messages/log_reader.cc [ 82%] Linking CXX shared module ../../../stage/lib/python3.11/dist-packages/ost/io/_ost_io.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-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/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gui/src/gl_win.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/sequence_viewer/align_properties_painter.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gl_canvas.hh:23, from /build/openstructure-2.3.1/modules/gui/src/gl_win.cc:25: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/aarch64-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, | ^~~~~~~~~ cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/io/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/io/pymod/remote.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./remote.pyc\",\"remote.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/io/pymod/repository.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/io/./repository.pyc\",\"repository.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 82%] Built target _ost_io make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 82%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_forcefield.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/view_op.hh:29, from /build/openstructure-2.3.1/modules/gui/src/scene_menu.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/sequence_viewer/base_row.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.cc [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/background_painter.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/conservation_painter.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/openstructure-2.3.1/modules/mol/mm/pymod/export_forcefield.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 82%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/secstr_row.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_forcefield.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_text_painter.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_delegate.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_model.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/sequence_row.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.cc:30: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_search_bar.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_table_view.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.cc [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_viewer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh:32, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.cc:31: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh:26, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh:28, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh:29, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/tick_painter.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.cc [ 83%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_settings.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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 83%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/title_row.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.cc /build/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/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/aarch64-linux-gnu/qt5/QtGui/qpainter.h:59, from /usr/include/aarch64-linux-gnu/qt5/QtGui/QPainter:1, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:30, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:35: /usr/include/aarch64-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:39: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/chain_view.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:28, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/openstructure-2.3.1/modules/mol/mm/pymod/export_settings.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( | ^~~~~~~~~~~~~~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/base_view_object.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.cc /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/sequence_viewer/sequence_view_object.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh:30: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc: In member function 'void ost::gui::SequenceViewer::MouseWheelEvent(QWheelEvent*)': /build/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/aarch64-linux-gnu/qt5/QtGui/QWheelEvent:1, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh:32, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.cc:42: /usr/include/aarch64-linux-gnu/qt5/QtGui/qevent.h:219:16: note: declared here 219 | inline int delta() const { return qt4D; } | ^~~~~ /build/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/aarch64-linux-gnu/qt5/QtGui/qevent.h:222:28: note: declared here 222 | inline Qt::Orientation orientation() const { return qt4O; } | ^~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/settings.hh:31, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_settings.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:26, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.cc:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27: /build/openstructure-2.3.1/obj-aarch64-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/algorithm:60, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qglobal.h:142, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QtCore:4, from /usr/include/aarch64-linux-gnu/qt5/QtGui/QtGuiDepends:3, from /usr/include/aarch64-linux-gnu/qt5/QtGui/QtGui:3, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_structure_segments.hh:25, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.hh:27, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/main_area.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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_area.cc.o -MF CMakeFiles/ost_gui.dir/main_area.cc.o.d -o CMakeFiles/ost_gui.dir/main_area.cc.o -c /build/openstructure-2.3.1/modules/gui/src/main_area.cc [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_state_saver.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/widget_state_saver.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh:32, from /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.cc:32: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/modules/gui/src/gosty_app.hh:28, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_selection.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/scene_selection.cc [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/widget_geom_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/widget_geom_handler.cc [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/file_loader.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/file_loader.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh:27, from /build/openstructure-2.3.1/modules/gui/src/gosty_app.cc:23: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh:23, from /build/openstructure-2.3.1/modules/gui/src/gosty_app.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /build/openstructure-2.3.1/modules/gui/src/gosty_app.cc:29: /build/openstructure-2.3.1/obj-aarch64-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/panels/button_bar.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/panels/button_bar.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/openstructure-2.3.1/modules/gui/src/gosty_app.cc:31: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qstring.h:49: /usr/include/aarch64-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) {} | ^~~~~~ [ 84%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/drop_box.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/panels/drop_box.cc [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/panels/panel_bar.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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/bottom_bar.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/panels/bottom_bar.cc [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/button_box.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/panels/button_box.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.hh:22, from /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/event_button.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/panels/event_button.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/view_op.hh:29, from /build/openstructure-2.3.1/modules/gui/src/scene_selection.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 85%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_simulation.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/modules/gui/src/file_loader.hh:24, from /build/openstructure-2.3.1/modules/gui/src/file_loader.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/modules/gui/src/file_loader.hh:30: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/openstructure-2.3.1/modules/gui/src/scene_selection.cc:34: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qstring.h:49, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/aarch64-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) {} | ^~~~~~ [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_manager.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/panels/panel_manager.cc [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_widget_container.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/panels/panel_widget_container.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/openstructure-2.3.1/modules/gui/src/file_loader.cc:51: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qstring.h:49, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/aarch64-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/openstructure-2.3.1/modules/gui/src/panels/event_button.cc: In member function 'virtual void ost::gui::EventButton::mouseMoveEvent(QMouseEvent*)': /build/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/aarch64-linux-gnu/qt5/QtGui/QDrag:1, from /build/openstructure-2.3.1/modules/gui/src/panels/event_button.cc:22: /usr/include/aarch64-linux-gnu/qt5/QtGui/qdrag.h:79:20: note: declared here 79 | Qt::DropAction start(Qt::DropActions supportedActions = Qt::CopyAction); | ^~~~~ [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/panel_bar_widget_holder.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/panels/panel_bar_widget_holder.cc [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/side_bar.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/panels/side_bar.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.hh:22, from /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/openstructure-2.3.1/modules/mol/mm/pymod/export_simulation.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/splitter_panel_bar.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/panels/splitter_panel_bar.cc [ 85%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/panels/tabbed_panel_bar.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/panels/tabbed_panel_bar.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:26, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_simulation.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : 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/tools/tool_option_group.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/tools/tool_option_group.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/system_creator.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/simulation.hh:27: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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( | ^~~~~~~~~~~~~~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/tools/tool_options.cc /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/tools/tool_option.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/tools/tool_option.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_manager.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/tools/tool_manager.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_win.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/tools/tool.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/mouse_event.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/tools/mouse_event.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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/manipulator.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/tools/manipulator.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.hh:24, from /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.cc:19: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/aarch64-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, | ^~~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_options_widget.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/tools/tool_options_widget.cc In file included from /build/openstructure-2.3.1/modules/gui/src/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/tool.cc:19: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/aarch64-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/openstructure-2.3.1/modules/gui/src/tools/mouse_event.cc:19: /build/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/aarch64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh:24: /usr/include/aarch64-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, | ^~~~~~~~~ [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/tool_bar.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/tools/tool_bar.cc [ 87%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/selection_tool.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/tools/selection_tool.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/tools/measure_tool.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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 /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/main_thread_runner.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.hh:26, from /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.cc:22: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh:27, from /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.cc:21: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh:26, from /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.cc:22: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/output_redirector.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, from /build/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( | ^~~~~~~~~~~~~~~~~~~~ [ 88%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_openmm.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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.hh:29, from /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.cc:29: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/aarch64-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/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc: In member function 'void ost::gui::OutputRedirector::Write(const String&)': /build/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/aarch64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.cc:25: /usr/include/aarch64-linux-gnu/qt5/QtCore/qdatetime.h:237:54: note: declared here 237 | QT_DEPRECATED_X("Use QElapsedTimer instead") int elapsed() const; | ^~~~~~~ /build/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/aarch64-linux-gnu/qt5/QtCore/qdatetime.h:236:54: note: declared here 236 | QT_DEPRECATED_X("Use QElapsedTimer instead") int restart(); | ^~~~~~~ /build/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/aarch64-linux-gnu/qt5/QtCore/qdatetime.h:235:55: note: declared here 235 | QT_DEPRECATED_X("Use QElapsedTimer instead") void start(); | ^~~~~ [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/completer_base.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/completer_base.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/dir_model.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh:24, from /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.cc:22: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/aarch64-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/python_shell/path_completer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/path_completer.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_context_parser.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/python_context_parser.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_completer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/python_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/openstructure-2.3.1/modules/mol/mm/pymod/export_openmm.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.cc: In constructor 'ost::gui::OstDirModel::OstDirModel(QObject*)': /build/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/aarch64-linux-gnu/qt5/QtWidgets/QDirModel:1, from /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.hh:26, from /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.cc:23: /usr/include/aarch64-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); | ^~~~~~~~~ [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.cc [ 88%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_interpreter_worker.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_model.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_namespace_tree_item.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_item.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_widget.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_shell_text_document_layout.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_text_document_layout.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/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/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( | ^~~~~~~~~~~~~~~~~~~~ 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/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ /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/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/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( | ^~~~~~~~~~~~~~~~~~~~ /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/openstructure-2.3.1/modules/gui/src/python_shell/python_namespace_tree_item.hh:25, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_tokenizer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, from /build/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( | ^~~~~~~~~~~~~~~~~~~~ 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/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ /build/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/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/aarch64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qstring.h:49, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:33: /usr/include/aarch64-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) {} | ^~~~~~ [ 89%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_observers.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/python_syntax_highlighter.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/python_syntax_highlighter.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/shell_history.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/shell_history.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/string_literal_positions.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/string_literal_positions.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/text_logger.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.cc /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc: In constructor 'ost::gui::PythonShellWidget::PythonShellWidget(QWidget*)': /build/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/aarch64-linux-gnu/qt5/QtWidgets/qwidget.h:50, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qframe.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qabstractscrollarea.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qtextedit.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qplaintextedit.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QPlainTextEdit:1, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:34: /usr/include/aarch64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ /build/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/aarch64-linux-gnu/qt5/QtWidgets/qplaintextedit.h:179:24: note: declared here 179 | QT_DEPRECATED void setTabStopWidth(int width); | ^~~~~~~~~~~~~~~ /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.cc: In member function 'void ost::gui::PythonShellWidget::SetTabWidth(int)': /build/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/aarch64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ /build/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/aarch64-linux-gnu/qt5/QtWidgets/qplaintextedit.h:179:24: note: declared here 179 | QT_DEPRECATED void setTabStopWidth(int width); | ^~~~~~~~~~~~~~~ [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state_machine.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/state_machine.cc [ 89%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition.cc.o [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/state.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/transition.cc cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/state.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/python_shell/transition_guard.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.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/openstructure-2.3.1/modules/mol/mm/pymod/export_observers.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( | ^~~~~~~~~~~~~~~~~~~~ [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/context_menu.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.cc /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/scene_win/current_selection_node.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/custom_part_node.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/io_profile.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/observer.hh:26, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_observers.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.hh:26, from /build/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 /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/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh:28, from /build/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( | ^~~~~~~~~~~~~~~~~~~~ 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/modules/gui/src/python_shell/transition.hh:23, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/observer.hh:33: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.hh:23, from /build/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/scene_node.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/scene_win/scene_node.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/label_node.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/scene_win/label_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/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.hh:24, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_node.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.cc [ 91%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/entity_part_node.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.cc [ 93%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_ff_reader.cc [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/scene_win/render_mode_node.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/entity.hh:29, from /build/openstructure-2.3.1/modules/gui/src/scene_win/label_node.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/openstructure-2.3.1/modules/gui/src/scene_win/label_node.hh:23, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.hh:23, from /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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/render_modes_node.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/scene_win/root_node.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:28, from /build/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node_fw.hh:25, from /build/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.hh:23, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/scene_win.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.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/openstructure-2.3.1/modules/mol/mm/pymod/export_ff_reader.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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/scene_win_model.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/forcefield.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/ff_reader.hh:32, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_ff_reader.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/argand.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/data_viewer/argand.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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.hh:23, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/argand.hh:30, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/argand.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.hh:28, from /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/view_type_fw.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/scene.hh:37, from /build/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/map_slab.hh:29, from /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/platform.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/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/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/aarch64-linux-gnu/qt5/QtCore/qobject.h:47, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QObject:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh:24, from /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.hh:34: /usr/include/aarch64-linux-gnu/qt5/QtCore/qstring.h:1511:20: note: declared here 1511 | inline QByteArray &QByteArray::append(const QString &s) | ^~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_selection.hh:23, from /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/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/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/aarch64-linux-gnu/qt5/QtCore/QModelIndex:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh:34, from /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.cc:26: /usr/include/aarch64-linux-gnu/qt5/QtCore/qabstractitemmodel.h:455:20: note: declared here 455 | inline QModelIndex QModelIndex::child(int arow, int acolumn) const | ^~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_interaction.cc [ 93%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/data_viewer_panel_base.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_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 /build/openstructure-2.3.1/obj-aarch64-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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/draw_overlay.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/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/drawing_functions.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.cc [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/fft_panel.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.hh:26, from /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc:28: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.cc:25: /usr/include/aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.hh:28, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/openstructure-2.3.1/modules/mol/mm/pymod/export_interaction.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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/normalizer_impl.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/norm_linear.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/norm.hh:30, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:36: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:37: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qstring.h:49, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33: /usr/include/aarch64-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/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/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/aarch64-linux-gnu/qt5/QtGui/QPixmapCache:1, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:40: /usr/include/aarch64-linux-gnu/qt5/QtGui/qpixmapcache.h:81:17: note: declared here 81 | static bool find(const QString &key, QPixmap &pixmap); | ^~~~ In file included from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.hh:37, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:41: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-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/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/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/aarch64-linux-gnu/qt5/QtCore/qobjectdefs.h:48, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qwindowdefs.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qwidget.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QWidget:1, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:46, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:34: /usr/include/aarch64-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/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/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/aarch64-linux-gnu/qt5/QtGui/QResizeEvent:1, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.cc:36: /usr/include/aarch64-linux-gnu/qt5/QtGui/qevent.h:219:16: note: declared here 219 | inline int delta() const { return qt4D; } | ^~~~~ /build/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/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/aarch64-linux-gnu/qt5/QtWidgets/qwidget.h:50: /usr/include/aarch64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ /build/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/aarch64-linux-gnu/qt5/QtGui/qfontmetrics.h:106:9: note: declared here 106 | int width(const QString &, int len = -1) const; | ^~~~~ /build/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/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/aarch64-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/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/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/aarch64-linux-gnu/qt5/QtWidgets/QDesktopWidget:1, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.cc:53: /usr/include/aarch64-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; | ^~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/fft.hh:27, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_interaction.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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 | ^~~~~~~~ [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/img2qt.cc.o /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.cc [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/mask_overlay.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.cc [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/null_overlay.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/data_viewer/null_overlay.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base.cc [ 94%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/overlay_manager.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_gui.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/circle_mask.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/mask_visitor.hh:28, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/pointlist_overlay.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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%] Building CXX object modules/gui/src/CMakeFiles/ost_gui.dir/data_viewer/viewer_normalizer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.cc [ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_buildingblock.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.hh:29, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/message.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh:34, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh:24, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay_base.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/module_config.hh:26, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_block_modifiers.cc [ 96%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o -MF CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o.d -o CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/pymod/export_topology.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/stat.hh:30, from /build/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.cc:30: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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%] Building CXX object modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -D_ost_mol_mm_EXPORTS -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-strong -Wformat -Werror=format-security 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/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/openstructure-2.3.1/modules/mol/mm/pymod/export_buildingblock.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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 96%] Linking CXX shared library ../../../stage/lib/libost_gui.so cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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 CMakeFiles/ost_gui.dir/moc_file_browser.cpp.o CMakeFiles/ost_gui.dir/moc_file_type_dialog.cpp.o CMakeFiles/ost_gui.dir/moc_file_viewer.cpp.o CMakeFiles/ost_gui.dir/moc_gl_canvas.cpp.o CMakeFiles/ost_gui.dir/moc_gl_win.cpp.o CMakeFiles/ost_gui.dir/moc_scene_menu.cpp.o CMakeFiles/ost_gui.dir/moc_gosty_app.cpp.o CMakeFiles/ost_gui.dir/moc_main.cpp.o CMakeFiles/ost_gui.dir/moc_main_area.cpp.o 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../../../stage/lib/libost_info.so.2.3.1 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so ../../../stage/lib/libost_base.so.2.3.1 ../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-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/openstructure-2.3.1/modules/mol/mm/pymod/export_block_modifiers.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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/buildingblock.hh:29, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_buildingblock.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/openstructure-2.3.1/modules/mol/mm/pymod/export_topology.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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/block_modifiers.hh:23, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_block_modifiers.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/openstructure-2.3.1/modules/mol/mm/pymod/export_modeller.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( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology.hh:31, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_topology.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/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/openstructure-2.3.1/modules/mol/mm/pymod/wrap_mol_mm.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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_topology.cc:22: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/block_modifiers.hh:23, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_modeller.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/modules/mol/mm/pymod/export_modeller.cc:22: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-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[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/depend make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod/CMakeFiles/_ost_gui.dir/DependInfo.cmake --color= [ 96%] Generating qrc_dngr.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/rcc --name dngr --output /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/qrc_dngr.cpp /build/openstructure-2.3.1/modules/gui/src/dngr.qrc [ 96%] Generating moc_gosty.cpp cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/lib/qt5/bin/moc @/build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_gosty.cpp_parameters make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/CMakeFiles/gosty.dir/DependInfo.cmake --color= [ 96%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_alignment_view.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_alignment_view.cc [ 96%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/wrap_gui.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/wrap_gui.cc [ 96%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_message_widget.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_message_widget.cc make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/gui/src/CMakeFiles/gosty.dir/build.make modules/gui/src/CMakeFiles/gosty.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] Building CXX object modules/gui/src/CMakeFiles/gosty.dir/gosty.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/gui/src/gosty.cc [ 96%] Building CXX object modules/gui/src/CMakeFiles/gosty.dir/moc_gosty.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/moc_gosty.cpp [ 96%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gl_win.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_gl_win.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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ /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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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/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 /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /build/openstructure-2.3.1/modules/gui/pymod/export_alignment_view.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 96%] Building CXX object modules/gui/src/CMakeFiles/gosty.dir/qrc_dngr.cpp.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/qrc_dngr.cpp [ 96%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_tool.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_tool.cc [ 96%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_py_shell.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_py_shell.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 96%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_gosty.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc [ 97%] Linking CXX executable ../../../stage/lib/openstructure/libexec/gosty cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_gui.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_gfx.so.2.3.1 /usr/lib/aarch64-linux-gnu/libOpenGL.so /usr/lib/aarch64-linux-gnu/libGLX.so /usr/lib/aarch64-linux-gnu/libGLU.so ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-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/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_regex.so make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 97%] Built target gosty [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_scene_win.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_perspective.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/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/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( | ^~~~~~~~~~~~~~~~~~~~ /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_sip_handler.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_sip_handler.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/modules/gui/pymod/export_tool.cc:25: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/aarch64-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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ 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/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 /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/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( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh:23, from /build/openstructure-2.3.1/modules/gui/pymod/export_scene_win.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/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/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 /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh:23, from /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /build/openstructure-2.3.1/modules/gui/pymod/export_sequence_viewer.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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( | ^~~~~~~~~~~~~~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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/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_selection.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_scene_selection.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh:27, from /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:30: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qbytearray.h:45, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qstring.h:50, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qdatetime.h:44, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QTime:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh:31, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gosty_app.hh:28, from /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:24: /usr/include/aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh:28, from /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:32: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:41, from /build/openstructure-2.3.1/modules/gui/pymod/export_gosty.cc:38: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qchar.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/qstring.h:49: /usr/include/aarch64-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/pymod/CMakeFiles/_ost_gui.dir/export_main_area.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_main_area.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_panels.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_panels.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_menu_bar.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_menu_bar.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/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 /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_view.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_view_wrapper.hh:24, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_selection.hh:23, from /build/openstructure-2.3.1/modules/gui/pymod/export_scene_selection.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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_file_loader.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_file_loader.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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_file_viewer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_file_viewer.cc [ 98%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_widget.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_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/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_gl_canvas.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/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/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/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( | ^~~~~~~~~~~~~~~~~~~~ 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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ /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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/file_loader.hh:24, from /build/openstructure-2.3.1/modules/gui/pymod/export_file_loader.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_data_viewer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_data_viewer.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/file_loader.hh:30: /build/openstructure-2.3.1/obj-aarch64-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/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("") | ^~~~~~~~~~~~~~~~~~~~~~~ [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_overlay.cc [100%] Building CXX object modules/gui/pymod/CMakeFiles/_ost_gui.dir/export_overlay_manager.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -I/usr/include/python3.11 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -fstack-protector-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/openstructure-2.3.1/modules/gui/pymod/export_overlay_manager.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh:30, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/gl_canvas.hh:23, from /build/openstructure-2.3.1/modules/gui/pymod/export_gl_canvas.cc:21: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qpoint.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtCore/QPoint:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh:24: /usr/include/aarch64-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/openstructure-2.3.1/modules/gui/pymod/sip_handler.hh:22, from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:30, from /build/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%] Linking CXX shared module ../../../../stage/lib/python3.11/dist-packages/ost/mol/mm/_ost_mol_mm.so cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/cmake -E cmake_link_script CMakeFiles/_ost_mol_mm.dir/link.txt --verbose=1 /usr/bin/c++ -fPIC -g -O2 -ffile-prefix-map=/build/openstructure-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/mm/_ost_mol_mm.so CMakeFiles/_ost_mol_mm.dir/export_forcefield.cc.o CMakeFiles/_ost_mol_mm.dir/export_settings.cc.o CMakeFiles/_ost_mol_mm.dir/export_simulation.cc.o CMakeFiles/_ost_mol_mm.dir/export_openmm.cc.o CMakeFiles/_ost_mol_mm.dir/export_observers.cc.o CMakeFiles/_ost_mol_mm.dir/export_ff_reader.cc.o CMakeFiles/_ost_mol_mm.dir/export_interaction.cc.o CMakeFiles/_ost_mol_mm.dir/export_buildingblock.cc.o CMakeFiles/_ost_mol_mm.dir/export_block_modifiers.cc.o CMakeFiles/_ost_mol_mm.dir/export_topology.cc.o CMakeFiles/_ost_mol_mm.dir/export_modeller.cc.o CMakeFiles/_ost_mol_mm.dir/wrap_mol_mm.cc.o -L/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../../stage/lib/libost_mol_mm.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_program_options.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 /usr/lib/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libOpenMM.so cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/mm/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/mol/mm/pymod/antechamber.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/mol/mm/./antechamber.pyc\",\"antechamber.py\",doraise=True)" 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/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( | ^~~~~~~~~~~~~~~~~~~~ make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' /usr/include/boost/detail/iterator.hpp:13:1: note: '#pragma message: This header is deprecated. Use instead.' 13 | BOOST_HEADER_DEPRECATED("") | ^~~~~~~~~~~~~~~~~~~~~~~ [100%] Built target _ost_mol_mm In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:35: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:33, from /build/openstructure-2.3.1/modules/gui/pymod/export_data_viewer.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /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/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 /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37, from /build/openstructure-2.3.1/modules/gui/pymod/data_viewer_proxy.hh:41: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qwidget.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QWidget:1, from /build/openstructure-2.3.1/modules/gui/pymod/sip_handler.hh:24: /usr/include/aarch64-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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh:37: /build/openstructure-2.3.1/obj-aarch64-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/aarch64-linux-gnu/qt5/QtCore/qglobal.h:1305, from /usr/include/aarch64-linux-gnu/qt5/QtGui/qtguiglobal.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qtwidgetsglobal.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/qmainwindow.h:43, from /usr/include/aarch64-linux-gnu/qt5/QtWidgets/QMainWindow:1, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/main_window.hh:35: /usr/include/aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point_list.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh:28, from /build/openstructure-2.3.1/modules/gui/pymod/export_overlay.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/presets.xml /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/scene/presets.xml cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/icons/color_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/scene/icons/color_icon.png cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/icons/preset_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/scene/icons/preset_icon.png cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/icons/render_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/scene/icons/render_icon.png cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/pymod/scene/icons/tool_icon.png /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/share/openstructure/scene/icons/tool_icon.png cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1=. -fstack-protector-strong 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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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib: ../../../stage/lib/libost_gui.so.2.3.1 /usr/lib/aarch64-linux-gnu/libpython3.11.so /usr/lib/aarch64-linux-gnu/libboost_python311.so ../../../stage/lib/libost_gfx.so.2.3.1 /usr/lib/aarch64-linux-gnu/libOpenGL.so /usr/lib/aarch64-linux-gnu/libGLX.so /usr/lib/aarch64-linux-gnu/libGLU.so ../../../stage/lib/libost_io.so.2.3.1 /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-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/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-linux-gnu/libboost_atomic.so ../../../stage/lib/libost_seq_alg.so.2.3.1 ../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so ../../../stage/lib/libost_mol.so.2.3.1 ../../../stage/lib/libost_info.so.2.3.1 /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_regex.so cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/color_options_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_options_widget.pyc\",\"color_options_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/color_select_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/color_select_widget.pyc\",\"color_select_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/combo_options_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/combo_options_widget.pyc\",\"combo_options_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/cpk_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/cpk_widget.pyc\",\"cpk_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/custom_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/custom_widget.pyc\",\"custom_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_editor_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_editor_widget.pyc\",\"gradient_editor_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_info_handler.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_info_handler.pyc\",\"gradient_info_handler.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_list_model.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_list_model.pyc\",\"gradient_list_model.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/gradient_preset_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/gradient_preset_widget.pyc\",\"gradient_preset_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/hsc_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/hsc_widget.pyc\",\"hsc_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/immutable_gradient_info_handler.py\",\"/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/immutable_preset_info_handler.py\",\"/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/init_inspector.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/init_inspector.pyc\",\"init_inspector.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/inspector_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/inspector_widget.pyc\",\"inspector_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/map_level_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/map_level_widget.pyc\",\"map_level_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/preset.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset.pyc\",\"preset.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/remote.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/remote.pyc\",\"remote.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/preset_editor_list_model.py\",\"/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/preset_editor_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_editor_widget.pyc\",\"preset_editor_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/preset_info_handler.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_info_handler.pyc\",\"preset_info_handler.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/preset_list_model.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_list_model.pyc\",\"preset_list_model.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/preset_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/preset_widget.pyc\",\"preset_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/render_mode_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_mode_widget.pyc\",\"render_mode_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/render_op.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_op.pyc\",\"render_op.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/render_options_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/render_options_widget.pyc\",\"render_options_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/scene_observer_impl.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_observer_impl.pyc\",\"scene_observer_impl.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/scene_selection_helper.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/scene_selection_helper.pyc\",\"scene_selection_helper.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/simple_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/simple_widget.pyc\",\"simple_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/sline_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/sline_widget.pyc\",\"sline_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/toolbar_options_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/toolbar_options_widget.pyc\",\"toolbar_options_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/trace_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/trace_widget.pyc\",\"trace_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/tube_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/tube_widget.pyc\",\"tube_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/uniform_color_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/uniform_color_widget.pyc\",\"uniform_color_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/visibility_op.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/visibility_op.pyc\",\"visibility_op.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/line_trace_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/line_trace_widget.pyc\",\"line_trace_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/wireframe_widget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/wireframe_widget.pyc\",\"wireframe_widget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/scene/query_editor.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/scene/query_editor.pyc\",\"query_editor.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/dng/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/dng/termuse.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/termuse.pyc\",\"termuse.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/dng/superpositiondialog.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/superpositiondialog.pyc\",\"superpositiondialog.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/dng/init.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/init.pyc\",\"init.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/dng/menu.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/dng/menu.pyc\",\"menu.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/__init__.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./__init__.pyc\",\"__init__.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/init_context_menu.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_context_menu.pyc\",\"init_context_menu.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/init_menubar.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_menubar.pyc\",\"init_menubar.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/init_spacenav.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_spacenav.pyc\",\"init_spacenav.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/init_splash.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./init_splash.pyc\",\"init_splash.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/trajectory_viewer.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./trajectory_viewer.pyc\",\"trajectory_viewer.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/helpwidget.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./helpwidget.pyc\",\"helpwidget.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/table.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./table.pyc\",\"table.py\",doraise=True)" cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod && /usr/bin/python3 -c "import py_compile;py_compile.compile(\"/build/openstructure-2.3.1/modules/gui/pymod/gosty_startup.py\",\"/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/gui/./gosty_startup.pyc\",\"gosty_startup.py\",doraise=True)" make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts/CMakeFiles/ost_scripts.dir/DependInfo.cmake --color= make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/build make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_config /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/openstructure/libexec/ost_config cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/bin/ost cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different dng /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/bin/dng cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_startup.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/ost_startup.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/scripts/dng_startup.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/dng_startup.py make[3]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [100%] Built target ost_scripts make[2]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' /usr/bin/cmake -E cmake_progress_start /build/openstructure-2.3.1/obj-aarch64-linux-gnu/CMakeFiles 0 make[1]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' dh_auto_test cd obj-aarch64-linux-gnu && make -j8 check ARGS\+=--verbose ARGS\+=-j8 make[1]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/openstructure-2.3.1 -B/build/openstructure-2.3.1/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 make -f CMakeFiles/Makefile2 check make[2]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' /usr/bin/cmake -S/build/openstructure-2.3.1 -B/build/openstructure-2.3.1/obj-aarch64-linux-gnu --check-build-system CMakeFiles/Makefile.cmake 0 /usr/bin/cmake -E cmake_progress_start /build/openstructure-2.3.1/obj-aarch64-linux-gnu/CMakeFiles 91 make -f CMakeFiles/Makefile2 CMakeFiles/check.dir/all make[3]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts/CMakeFiles/subst_ost_startup.py.dir/DependInfo.cmake --color= make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src/CMakeFiles/create_stage.dir/DependInfo.cmake --color= 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[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts/CMakeFiles/subst_ost_config.dir/DependInfo.cmake --color= make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts/CMakeFiles/subst_ost.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts/CMakeFiles/subst_dng.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/subst_dng.dir/build.make scripts/CMakeFiles/subst_dng.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/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/openstructure-2.3.1/cmake_support/substitute.cmake make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/base/src/CMakeFiles/create_stage.dir/build.make modules/base/src/CMakeFiles/create_stage.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/subst_ost_startup.py.dir/build.make scripts/CMakeFiles/subst_ost_startup.py.dir/build make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/subst_ost_config.dir/build.make scripts/CMakeFiles/subst_ost_config.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/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/openstructure-2.3.1/cmake_support/substitute.cmake make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/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/openstructure-2.3.1/cmake_support/substitute.cmake make -f scripts/CMakeFiles/subst_ost.dir/build.make scripts/CMakeFiles/subst_ost.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/bin make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -DINPUT_FILE=/build/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/openstructure-2.3.1/cmake_support/substitute.cmake make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/openstructure/libexec [ 0%] Built target subst_dng make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 0%] Built target subst_ost_startup.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E make_directory /build/openstructure-2.3.1/obj-aarch64-linux-gnu/tests [ 0%] Built target subst_ost_config make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 0%] Built target subst_ost [ 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[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg_headers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom_headers.dir/DependInfo.cmake --color= 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/config /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/config /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/config/CMakeFiles/ost_config_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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src/CMakeFiles/ost_base_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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src/CMakeFiles/ost_info_headers.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol_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]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq_headers.dir/DependInfo.cmake --color= 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]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./alignment_opts.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./alignment_opts.hh make -f modules/config/CMakeFiles/ost_config_headers.dir/build.make modules/config/CMakeFiles/ost_config_headers.dir/build make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./base.hh 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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info.hh make -f modules/geom/src/CMakeFiles/ost_geom_headers.dir/build.make modules/geom/src/CMakeFiles/ost_geom_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/export_helper/vector.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/export_helper/vector.hh make -f modules/conop/src/CMakeFiles/ost_conop_headers.dir/build.make modules/conop/src/CMakeFiles/ost_conop_headers.dir/depend make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src/CMakeFiles/ost_conop_headers.dir/DependInfo.cmake --color= make -f modules/base/src/CMakeFiles/ost_base_headers.dir/build.make modules/base/src/CMakeFiles/ost_base_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/generic_property_def.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/export_helper/generic_property_def.hh 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]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/pointer_iterator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/pointer_iterator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./clip_alignment.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./clip_alignment.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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 cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./config.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_error.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_error.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./conop.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./conop.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_group.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_group.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./dllexport.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./dllexport.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./def.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./def.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./conservation.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./conservation.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/pair_to_tuple_conv.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/export_helper/pair_to_tuple_conv.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./processor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./processor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_prop.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_prop.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/config && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/config/./version.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./version.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./exc.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./exc.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/export_helper/vec_to_list_conv.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/export_helper/vec_to_list_conv.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./contact_prediction_score.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./contact_prediction_score.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/test_utils/compare_files.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/test_utils/compare_files.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./amino_acids.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./amino_acids.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./geom.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./geom.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/impl/sequence_list_iterator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/impl/sequence_list_iterator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/atom_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/atom_impl_fw.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./contact_weight_matrix.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./contact_weight_matrix.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./generic_property.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./generic_property.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./diag.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./diag.hh [ 0%] Built target ost_config_headers make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./distance_map.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./distance_map.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src/CMakeFiles/ost_db_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./mat.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./integrity_error.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./integrity_error.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_list.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./sequence_list.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/chain_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./model_check.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./model_check.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./invalid_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./invalid_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat2.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./mat2.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./entropy.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./entropy.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_group.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_group.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/db/src/CMakeFiles/ost_db_headers.dir/build.make modules/db/src/CMakeFiles/ost_db_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./sqlite_wrap.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/db/./sqlite_wrap.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/chain_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/chain_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./ptr_observer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./ptr_observer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./heuristic.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./heuristic.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./sequence_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./global_align.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./global_align.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat3.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./mat3.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_item.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_item.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./sqlite_conv.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/db/./sqlite_conv.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./compound.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./log.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./log.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/connector_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./alignment_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./alignment_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./ins_del.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./ins_del.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/db/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./mat4.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./mat4.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound_lib.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./compound_lib.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./log_sink.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./log_sink.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/connector_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/connector_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./local_align.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./local_align.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./linear_indexer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/db/./linear_indexer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_path.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_path.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./profile.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./profile.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/dihedral.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/dihedral.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./sequence_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./sequence_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./merge_pairwise_alignments.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./merge_pairwise_alignments.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./rule_based.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./rule_based.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_region.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./aligned_region.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./binary_container.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/db/./binary_container.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec2.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec2.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_column.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./aligned_column.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./dyn_cast.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./dyn_cast.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_set.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_set.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec3.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec3.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./minimal_compound_lib.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./minimal_compound_lib.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/db/src/./extract_data_helper.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/db/./extract_data_helper.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./aligned_column_iterator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./aligned_column_iterator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_visitor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_visitor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./stdint.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./stdint.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./compound_lib_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./compound_lib_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/entity_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/entity_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec4.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec4.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./invalid_sequence.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./invalid_sequence.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./pair_subst_weight_matrix.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./pair_subst_weight_matrix.hh [ 0%] Built target ost_db_headers cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./stdint_msc.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./stdint_msc.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./info_verbose_visitor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./info_verbose_visitor.hh make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./views_from_sequences.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./views_from_sequences.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/conop/src/./ring_finder.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/./ring_finder.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vecmat_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/fragment_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./item_type.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./item_type.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./semiglobal_align.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./semiglobal_align.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./range.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./range.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/base/src/./profile_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/./profile_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat2_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vecmat2_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/fragment_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/fragment_impl_fw.hh [ 0%] Built target ost_conop_headers make -f modules/img/base/src/CMakeFiles/ost_img_headers.dir/build.make modules/img/base/src/CMakeFiles/ost_img_headers.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./sequence_identity.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./sequence_identity.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./geom_info_conversion.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./geom_info_conversion.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./module_config.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat3_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vecmat3_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/query_ast.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_gen_s.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_iso_gen_s.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./sequence_similarity.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./sequence_similarity.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/info/src/./item_type_cast.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/info/./item_type_cast.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vecmat4_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vecmat4_op.hh [ 0%] Built target ost_seq_headers make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_ast_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/query_ast_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./units.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./units.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/raster_image/raster_image.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/raster_image/raster_image.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 make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_iso_spec.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_iso_spec.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./subst_weight_matrix.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./subst_weight_matrix.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/dispatch.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/dispatch.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./message.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./message.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/map_octree.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/query_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./circular_iterator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./circular_iterator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./platform.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./platform.hh [ 0%] Built target ost_info_headers cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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 make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./anisotropic.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./anisotropic.hh make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/query_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/query_impl_fw.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./variance_map.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./variance_map.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/octree_isocont.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/octree_isocont.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./constants.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./constants.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/gui/src/CMakeFiles/ost_gui_headers.dir/build.make modules/gui/src/CMakeFiles/ost_gui_headers.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./string_ref.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./string_ref.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./auto_correlate.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./auto_correlate.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./data/default_contact_weight_matrix.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./default_contact_weight_matrix.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/cartoon_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/cartoon_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/residue_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite2.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite2.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_option_group.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_option_group.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./data/default_pair_subst_weight_matrix.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./default_pair_subst_weight_matrix.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./pod_vector.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./pod_vector.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./clear.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./clear.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/custom_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/custom_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite3.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite3.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/residue_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/residue_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./hmm_pseudo_counts.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./hmm_pseudo_counts.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./clip_min_max.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./clip_min_max.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./fixed_string.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./fixed_string.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/cpk_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/cpk_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_base_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_base_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_bar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_bar.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/surface_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./conjugate.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./conjugate.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/debug_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/debug_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/seq/alg/src/./hmm_score.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/./hmm_score.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./tri_matrix.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./tri_matrix.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite2_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite2_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/selection_tool.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/selection_tool.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_def.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/surface_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/surface_impl_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/simple_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/simple_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./convolute.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./convolute.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./boost_filesystem_helper.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./boost_filesystem_helper.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_factory.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_factory.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./composite3_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./composite3_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/measure_tool.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/measure_tool.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/sline_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/sline_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./correlate.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./correlate.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 cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/torsion_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./aligned_cuboid.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./aligned_cuboid.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src/CMakeFiles/ost_io_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/base/src/./paged_array.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/./paged_array.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_frequency_domain.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_frequency_domain.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_option.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_option.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./vec_mat_predicates.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./vec_mat_predicates.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./cross_correlate.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./cross_correlate.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/impl/torsion_impl_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/impl/torsion_impl_fw.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/io/src/CMakeFiles/ost_io_headers.dir/build.make modules/io/src/CMakeFiles/ost_io_headers.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_half_frequency_domain.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_half_frequency_domain.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/chemdict_parser.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/chemdict_parser.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/line_trace_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/line_trace_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./quat.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./quat.hh [ 0%] Built target ost_base_headers 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src/CMakeFiles/ost_mol_alg_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_manager.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_manager.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./density_slice.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./density_slice.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/star_parser.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/star_parser.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/backbone_trace.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/backbone_trace.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./atom_base.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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 make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./svd_superpose.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./svd_superpose.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./transform.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./transform.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./dft.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./dft.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_widget.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_options_widget.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_spatial_domain.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_detail.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_detail.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./atom_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/mmcif_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/manipulator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/manipulator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fft.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fft.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./point_cloud.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./point_cloud.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fftw_helper.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fftw_helper.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./atom_view.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./atom_view.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/tool_options_win.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/tool_options_win.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/mmcif_info.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_algorithm.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_algorithm.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/geom/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./sec_structure_segments.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./sec_structure_segments.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/trace_renderer_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/trace_renderer_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/mouse_event.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/mouse_event.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fill.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fill.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/tools/map_tool.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/tools/map_tool.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bond_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./bond_handle.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/image_state_visitor_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_visitor_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./local_dist_diff_test.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./local_dist_diff_test.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/io_profile.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/io_profile.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/connect_renderer_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/connect_renderer_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./filter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./filter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/dcd_io.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/index.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/index.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bond_table.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./bond_table.hh [ 0%] Built target ost_geom_headers cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/align_properties_painter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/align_properties_painter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./distance_test_common.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./distance_test_common.hh make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/type_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/type_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/mapped_property.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/mapped_property.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_crd_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_crd_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fourier_filters.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fourier_filters.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./chain_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_row.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_row.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/image_state/value_holder.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/value_holder.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./distance_rmsd_test.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./distance_rmsd_test.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings_headers.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/entity_renderer_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/entity_renderer_fw.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/bindings/src/./wrap_tmalign.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/bindings/./wrap_tmalign.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pqr_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_pqr_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./algorithm.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./algorithm.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/tabulated_trig.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/tabulated_trig.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./superpose_frames.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./superpose_frames.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./chain_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mae_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_mae_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./circle_mask.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./circle_mask.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/impl/fast_spheres.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/fast_spheres.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/background_painter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/background_painter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian_gradient_magnitude.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./gaussian_gradient_magnitude.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_view.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./chain_view.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./filter_clashes.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./filter_clashes.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/line_render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/line_render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/conservation_painter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/conservation_painter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_mmcif_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_mmcif_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./gaussian.hh [ 0%] Built target ost_bindings_headers cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chain_type.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./chain_type.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./composite_mask.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./composite_mask.hh make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/custom_render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/custom_render_options.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/painter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/painter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./construct_cbeta.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./construct_cbeta.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chem_class.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./chem_class.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./gaussian_laplacian.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./gaussian_laplacian.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/cpk_render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/cpk_render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_algorithm.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./data_algorithm.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./clash_score.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./clash_score.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm_headers.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/secstr_row.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/secstr_row.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./chem_type.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./chem_type.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./forcefield.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./forcefield.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/simple_render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/simple_render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./trajectory_analysis.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./trajectory_analysis.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_observer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./data_observer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./highest_peak_search_3d.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./highest_peak_search_3d.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_secstr_painter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_secstr_painter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_group.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./coord_group.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_pdb_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_pdb_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/sline_render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/sline_render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./structure_analysis.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./structure_analysis.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./ff_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./ff_reader.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_writer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_writer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./histogram.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./histogram.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data_types.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./data_types.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/entity_io_sdf_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/entity_io_sdf_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_selection_painter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_selection_painter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_source.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./coord_source.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./buildingblock.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./buildingblock.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/line_trace_render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/line_trace_render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./line_iterator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./line_iterator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./data.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./data.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/seq_text_painter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/seq_text_painter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./pdbize.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./pdbize.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/sdf_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/sdf_reader.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/cartoon_render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/cartoon_render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./in_mem_coord_source.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./in_mem_coord_source.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./debug.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./debug.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./block_modifiers.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./block_modifiers.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./local_sigma_threshold.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./local_sigma_threshold.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./adjacency_bitmap.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./adjacency_bitmap.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./coord_frame.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./coord_frame.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./dllexport.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./dllexport.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_delegate.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_delegate.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./gromacs_block_modifiers.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./gromacs_block_modifiers.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/render_options/trace_render_options.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/render_options/trace_render_options.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/sdf_writer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/sdf_writer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent_iterator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./extent_iterator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./mask_image.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./mask_image.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_model.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_model.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./editor_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./editor_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./consistency_checks.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./consistency_checks.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./heuristic_block_modifiers.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./heuristic_block_modifiers.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/save_entity.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/save_entity.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent_mask.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./extent_mask.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./editor_type_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./editor_type_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./negate.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./negate.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./interaction.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./interaction.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./contact_overlap.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./contact_overlap.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_row.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_row.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_element_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/by_element_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./extent.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./extent.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./mol.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./mol.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/load_entity.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/load_entity.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./normalizer_factory.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./normalizer_factory.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_factory.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image_factory.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/by_chain_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/by_chain_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_search_bar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_search_bar.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./domain_find.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./domain_find.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./settings.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./settings.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./norm.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/surface_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/surface_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_table_view.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_table_view.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/load_surface.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/load_surface.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./similarity_matrix.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./similarity_matrix.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/uniform_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/uniform_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./normalizer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./normalizer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./simulation.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./simulation.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_viewer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_viewer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./accessibility.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./accessibility.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_handle_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image_handle_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./modeller.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./modeller.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_linear.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./norm_linear.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/surface_io_msms_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/surface_io_msms_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_log.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./norm_log.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./sec_struct.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./sec_struct.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/tick_painter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/tick_painter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_observer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_observer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/entity_view_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/entity_view_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./norm_od.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./norm_od.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./nonstandard.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./nonstandard.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./observer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./observer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/pdb_str.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_str.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_observer_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_observer_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/basic_gradient_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/basic_gradient_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/title_row.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/title_row.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./power_spectrum.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./power_spectrum.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./molck.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./molck.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/stereochemical_params_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/stereochemical_params_reader.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_list.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image_list.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_property_mapper.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_property_mapper.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./state_extractor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./state_extractor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/alignment_view_object.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/alignment_view_object.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./randomize.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./randomize.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/gradient_level_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/gradient_level_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/mol/omf.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/omf.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_view.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_view.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./system_creator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./system_creator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./find_membrane.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./find_membrane.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_state_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image_state_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/base_view_object.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/base_view_object.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/load_map.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/load_map.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./smooth_mask_image.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./smooth_mask_image.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/color_ops/map_handle_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color_ops/map_handle_color_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/alg/src/./entity_to_density.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/./entity_to_density.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./topology_creator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./topology_creator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_visitor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_visitor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image_state.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image_state.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./render_pass.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./render_pass.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/sequence_viewer/sequence_view_object.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/sequence_viewer/sequence_view_object.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./index.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./index.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./image.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./image.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./stat.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_df3_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_df3_handler.hh [ 0%] Built target ost_mol_alg_headers cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./entity_visitor_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./entity_visitor_fw.hh make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./bitmap_io.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./bitmap_io.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./topology.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./topology.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/config /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/config /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/config/CMakeFiles/ost_config.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/main_thread_runner.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/main_thread_runner.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/image_format.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/image_format.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./inverted_mask.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./inverted_mask.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat_accumulator.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./stat_accumulator.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./collada_exporter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./collada_exporter.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/config/CMakeFiles/ost_config.dir/build.make modules/config/CMakeFiles/ost_config.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/config/CMakeFiles/ost_config.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./handle_type_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./handle_type_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/output_redirector.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/output_redirector.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./stat_min_max.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./stat_min_max.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./map.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./map.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/mm/src/./steep.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/./steep.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./ics_editor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./ics_editor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dx_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_dx_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/completer_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/completer_base.hh [ 0%] Built target ost_config cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./color.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./color.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_base_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_base_fw.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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/src/CMakeFiles/ost_geom.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./threshold.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./threshold.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./not_connected_error.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./not_connected_error.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_spi_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_spi_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/dir_model.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/dir_model.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./entity.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./entity.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transcendentals.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transcendentals.hh [ 0%] Built target ost_mol_mm_headers cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./property_id.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./property_id.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/gutter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/gutter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./entity_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./entity_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_situs_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_situs_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transform.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transform.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./query.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/path_completer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/path_completer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gl_helper.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gl_helper.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/geom/src/CMakeFiles/ost_geom.dir/build.make modules/geom/src/CMakeFiles/ost_geom.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_visitor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_visitor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_context_parser.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_context_parser.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_mrc_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_mrc_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transform_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transform_fw.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/geom/src/CMakeFiles/ost_geom.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_error.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./query_error.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./mask.hh [ 2%] Built target ost_geom cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_completer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_completer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dat_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_dat_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_transform.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./alg_transform.hh make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/src/CMakeFiles/ost_base.dir/DependInfo.cmake --color= make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/pymod/CMakeFiles/_ost_geom.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_shell.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_state.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./query_state.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_mirror.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./alg_mirror.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_ipl_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_ipl_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./residue_base.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/base/src/CMakeFiles/ost_base.dir/build.make modules/base/src/CMakeFiles/ost_base.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_jpk_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_jpk_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./normalizer_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./normalizer_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./alg_shift.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./alg_shift.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_node_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_widget.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_widget.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./residue_handle.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/base/src/CMakeFiles/ost_base.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_nanoscope_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_nanoscope_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./discrete_shrink.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./discrete_shrink.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_tokenizer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_tokenizer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./normalizer_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./normalizer_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_node_visitor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_node_visitor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_prop.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./residue_prop.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_png_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_png_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_object_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transformation_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transformation_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./null_data.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./null_data.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_syntax_highlighter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_syntax_highlighter.hh [ 3%] Built target ost_base 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests/CMakeFiles/ost_geom_tests.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_object.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./residue_view.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./residue_view.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_dm3_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_dm3_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./observable.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./observable.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./transformations.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./transformations.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/text_logger.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/text_logger.hh [ 3%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite3.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_object_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_object_fw.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./fractional_shift.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./fractional_shift.hh make -f modules/geom/pymod/CMakeFiles/_ost_geom.dir/build.make modules/geom/pymod/CMakeFiles/_ost_geom.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/map_io_tiff_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/map_io_tiff_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./paste_impl.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./paste_impl.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-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/openstructure-2.3.1/modules/geom/tests/test_composite3.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./sec_structure.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./sec_structure.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./peak.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./peak.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./spatial_organizer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./spatial_organizer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_prim.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_prim.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/tiff_util.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/tiff_util.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./surface.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./phase.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./phase.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_interpreter_worker.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_interpreter_worker.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./symmetry_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./symmetry_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/img/jpk_util.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/jpk_util.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_builder.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./surface_builder.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./polar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./polar.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./physical_units.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./physical_units.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gfx_test_object.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gfx_test_object.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/geom/pymod/CMakeFiles/_ost_geom.dir/build'. cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./builder.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./builder.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/python_shell_text_document_layout.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/python_shell_text_document_layout.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/sequence_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./line_average.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./line_average.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./pixel_sampling.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./pixel_sampling.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/shell_history.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/shell_history.hh [ 5%] Built target _ost_geom cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./glwin_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./glwin_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/alg/src/./rscrosscorr.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/./rscrosscorr.hh make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/src/CMakeFiles/ost_info.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/state_machine.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/state_machine.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./surface_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/fasta_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/fasta_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./input.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./input.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./point_list.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./point_list.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./surface_prop.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./surface_prop.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./point.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./point.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./prim_list.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./prim_list.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/state.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/state.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/pir_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh [ 5%] Built target ost_img_alg_headers make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/info/src/CMakeFiles/ost_info.dir/build.make modules/info/src/CMakeFiles/ost_info.dir/build make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/pymod/CMakeFiles/_ost_base.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./polygon_mask.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./polygon_mask.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./scene.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./scene.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./torsion_handle.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./torsion_handle.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/transition.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/transition.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/info/src/CMakeFiles/ost_info.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/promod_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/promod_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./progress.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./progress.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./transfer_connectivity.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./transfer_connectivity.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./selection.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./selection.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/profile_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/profile_io_handler.hh [ 6%] Built target ost_info cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/python_shell/transition_guard.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/python_shell/transition_guard.hh [ 6%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_composite2.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-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/openstructure-2.3.1/modules/geom/tests/test_composite2.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./surface.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./surface.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./size.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./size.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/button_bar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/button_bar.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./query_view_wrapper.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./query_view_wrapper.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/hhm_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/hhm_io_handler.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/base/pymod/CMakeFiles/_ost_base.dir/build.make modules/base/pymod/CMakeFiles/_ost_base.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./texture.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./texture.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./spherical_mask.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./spherical_mask.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/drop_box.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/drop_box.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./view_op.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/base/pymod/CMakeFiles/_ost_base.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/pssm_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/pssm_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./vertex_array.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./vertex_array.hh [ 6%] Built target _ost_base cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_type_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./view_type_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./util.cc /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./util.cc make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/panel_bar.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/info/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/info/pymod/CMakeFiles/_ost_info.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./vertex_array_helper.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./vertex_array_helper.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./util.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./util.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/clustal_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./scene_observer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./scene_observer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./view_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./view_op.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/load.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/load.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_manager.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/panel_manager.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/info/pymod/CMakeFiles/_ost_info.dir/build.make modules/info/pymod/CMakeFiles/_ost_info.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./value_util.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./value_util.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gl_include.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gl_include.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/info/pymod/CMakeFiles/_ost_info.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/seq/save.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/save.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./xcs_editor.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./xcs_editor.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/bottom_bar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/bottom_bar.hh [ 6%] Built target _ost_info cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./binary_data_sink.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./binary_data_sink.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./vecmat.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./vecmat.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./glext_include.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./glext_include.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./bounding_box.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./bounding_box.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_manager.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./io_manager.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/button_box.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/button_box.hh [ 6%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat2.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/img/base/src/./mask_info_convert.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/./mask_info_convert.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-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/openstructure-2.3.1/modules/geom/tests/test_mat2.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./transform.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./transform.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./render_mode.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./render_mode.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./binary_data_source.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./binary_data_source.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/event_button.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/event_button.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/mol/base/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./material.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./material.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_widget_container.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/panel_widget_container.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gradient.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gradient.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./container_serialization.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./container_serialization.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 6%] Built target ost_img_headers make -f modules/img/base/src/CMakeFiles/ost_img.dir/build.make modules/img/base/src/CMakeFiles/ost_img.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/panel_bar_widget_holder.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/panel_bar_widget_holder.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/src/CMakeFiles/ost_img.dir/DependInfo.cmake --color= [ 6%] Built target ost_mol_headers cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gradient_manager.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gradient_manager.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./swap_util.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./swap_util.hh 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/src/CMakeFiles/ost_mol.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_utils.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./io_utils.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/side_bar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/side_bar.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./io_exception.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./io_exception.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./primitives.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./primitives.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./convert.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./convert.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/splitter_panel_bar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/splitter_panel_bar.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./povray_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./povray_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./converting_streams.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./converting_streams.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/panels/tabbed_panel_bar.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/panels/tabbed_panel_bar.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/context_menu.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/context_menu.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./povray.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./povray.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./formatted_line.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./formatted_line.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/current_selection_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/current_selection_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./exporter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./exporter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/chemdict_parser.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./chemdict_parser.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./exporter_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./exporter_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/custom_part_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/custom_part_node.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/star_parser.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./star_parser.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/entity_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./gost_exporter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./gost_exporter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/mmcif_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./mmcif_reader.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/entity_part_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/entity_part_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./color_ops/map_handle_color_op.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./map_handle_color_op.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/img/base/src/CMakeFiles/ost_img.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/gfx_scene_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/gfx_scene_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/mmcif_info.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./mmcif_info.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_iso.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./map_iso.hh [ 9%] 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[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/src/CMakeFiles/ost_img_alg.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/label_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/label_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/io_profile.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./io_profile.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_slab.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./map_slab.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/root_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/root_node.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gfx/src/./map_iso_prop.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/./map_iso_prop.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/dcd_io.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./dcd_io.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/render_mode_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/render_mode_node.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/render_modes_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/render_modes_node.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_crd_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_crd_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_pqr_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_pqr_handler.hh [ 9%] Built target ost_gfx_headers cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_node.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_node.hh 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/pymod/CMakeFiles/_ost_img.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_mae_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_mae_handler.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/base/src/CMakeFiles/ost_mol.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_mmcif_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_mmcif_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/scene_win/scene_win_model.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/scene_win/scene_win_model.hh [ 15%] Built target ost_mol 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/src/CMakeFiles/ost_seq.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/message_widget.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/messages/message_widget.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/message_box_widget.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/messages/message_box_widget.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./pdb_reader.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_pdb_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_pdb_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/messages/log_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/messages/log_reader.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_writer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./pdb_writer.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/argand.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/argand.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/seq/base/src/CMakeFiles/ost_seq.dir/build.make modules/seq/base/src/CMakeFiles/ost_seq.dir/build make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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 cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/entity_io_sdf_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./entity_io_sdf_handler.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/seq/base/src/CMakeFiles/ost_seq.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/sdf_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./sdf_reader.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel.hh [ 16%] Built target ost_seq make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/data_viewer_panel_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/data_viewer_panel_base.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/img/base/pymod/CMakeFiles/_ost_img.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/sdf_writer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./sdf_writer.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/img/alg/src/CMakeFiles/ost_img_alg.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 17%] Built target _ost_img make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/src/CMakeFiles/ost_db.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/draw_overlay.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/draw_overlay.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/save_entity.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./save_entity.hh [ 21%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/tests/CMakeFiles/ost_base_tests.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/load_entity.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./load_entity.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/drawing_functions.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/drawing_functions.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/db/src/CMakeFiles/ost_db.dir/build.make modules/db/src/CMakeFiles/ost_db.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/surface_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./surface_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/fft_panel.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/fft_panel.hh [ 21%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_generic_property.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/tests/test_generic_property.cc make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/db/src/CMakeFiles/ost_db.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/info_panel.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/info_panel.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/load_surface.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./load_surface.hh [ 21%] Built target ost_db make -f modules/bindings/src/CMakeFiles/ost_bindings.dir/build.make modules/bindings/src/CMakeFiles/ost_bindings.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/src/CMakeFiles/ost_bindings.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/img2qt.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/img2qt.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/surface_io_msms_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./surface_io_msms_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/mask_overlay.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/mask_overlay.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/bindings/src/CMakeFiles/ost_bindings.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/pdb_str.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./pdb_str.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/null_overlay.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/null_overlay.hh [ 21%] Built target ost_bindings 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/tests/CMakeFiles/ost_img_tests.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/stereochemical_params_reader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./stereochemical_params_reader.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 23%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_data.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./mol/omf.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./omf.hh cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/base/tests/test_data.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/sequence_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./sequence_io_handler.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build.make modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_base_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_base_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/fasta_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./fasta_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/pir_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./pir_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/promod_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./promod_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_gui.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_gui.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/profile_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./profile_io_handler.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/base/pymod/CMakeFiles/_ost_mol.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/overlay_manager_observer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/overlay_manager_observer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/hhm_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./hhm_io_handler.hh [ 25%] Built target _ost_mol 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 cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/pssm_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./pssm_io_handler.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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 cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/pointlist_overlay_base.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/pointlist_overlay_base.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/clustal_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./clustal_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/strategies.hh [ 25%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_clear.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/load.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./load.hh cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/alg/tests/test_clear.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/strategies_fw.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/strategies_fw.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./seq/save.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./save.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/data_viewer/viewer_normalizer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/data_viewer/viewer_normalizer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/load_map.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./load_map.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_browser.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./file_browser.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_type_dialog.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./file_type_dialog.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_df3_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_df3_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_viewer.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./file_viewer.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/image_format.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./image_format.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gl_canvas.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./gl_canvas.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dx_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_dx_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gl_win.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./gl_win.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_spi_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_spi_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./scene_menu.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./scene_menu.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_situs_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_situs_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./gosty_app.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./gosty_app.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./admin.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./admin.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_mrc_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_mrc_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./module_config.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./module_config.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dat_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_dat_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./main.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_ipl_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_ipl_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main_area.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./main_area.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_jpk_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_jpk_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./perspective.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./perspective.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_nanoscope_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_nanoscope_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./scene_selection.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./scene_selection.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_png_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_png_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./main_window.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./main_window.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_dm3_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_dm3_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./dock_widget.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./dock_widget.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/map_io_tiff_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./map_io_tiff_handler.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./dock_widget.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./dock_widget.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/tiff_util.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./tiff_util.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./thin_splitter.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./thin_splitter.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/io/src/./img/jpk_util.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/./jpk_util.hh cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_geom_handler.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget_geom_handler.hh [ 25%] Built target ost_io_headers make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/depend cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_pool.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget_pool.hh make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/DependInfo.cmake --color= cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_registry.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget_registry.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./widget_state_saver.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./widget_state_saver.hh [ 25%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_atom_groups.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/base/tests/test_atom_groups.cc cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/modules/gui/src/./file_loader.hh /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gui/./file_loader.hh make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 25%] Built target ost_gui_headers 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 25%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_sequence.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/seq/base/tests/test_sequence.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_composite3.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_composite2.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_mat2.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/modules/img/base/tests/test_data.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/modules/img/base/tests/test_data.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/base/tests/test_generic_property.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_clear.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_atom_groups.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/seq/base/tests/test_sequence.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/base/tests/CMakeFiles/ost_img_tests.dir/test_extent.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/base/tests/test_extent.cc [ 25%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_mat3.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-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/openstructure-2.3.1/modules/geom/tests/test_mat3.cc [ 25%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_conj.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/alg/tests/test_conj.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/img/base/tests/test_extent.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_mat4.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-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/openstructure-2.3.1/modules/geom/tests/test_mat4.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_mat3.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_conj.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_mat4.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_chain.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc [ 25%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op2.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-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/openstructure-2.3.1/modules/geom/tests/test_op2.cc [ 25%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/base/tests/test_image.cc [ 25%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/test_string_ref.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/tests/test_string_ref.cc [ 25%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_convolute.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/alg/tests/test_convolute.cc [ 25%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_op3.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-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/openstructure-2.3.1/modules/geom/tests/test_op3.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_op2.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_op4.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-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/openstructure-2.3.1/modules/geom/tests/test_op4.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/base/tests/test_image.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_column.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_convolute.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_op3.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_op4.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_quat.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-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/openstructure-2.3.1/modules/geom/tests/test_quat.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/alg/tests/test_discrete_shrink.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:28: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_column.cc:29: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_vec3.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-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/openstructure-2.3.1/modules/geom/tests/test_vec3.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_discrete_shrink.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_vec2.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_vec3.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/img/base/tests/CMakeFiles/ost_img_tests.dir/test_image_state.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/base/tests/test_image_state.cc [ 26%] Building CXX object modules/base/tests/CMakeFiles/ost_base_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/base/tests/tests.cc [ 26%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fft.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/alg/tests/test_fft.cc [ 26%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_vec4.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-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/openstructure-2.3.1/modules/geom/tests/test_vec4.cc [ 26%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_aligned_region.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc [ 26%] Linking CXX executable ../../../tests/ost_base_tests cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 26%] Built target ost_base_tests [ 26%] Building CXX object modules/geom/tests/CMakeFiles/ost_geom_tests.dir/test_transform.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-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/openstructure-2.3.1/modules/geom/tests/test_transform.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/extent.hh:34, from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state.cc:32: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/modules/geom/tests/test_vec4.cc:20: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec2.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec.hh:24, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/tests.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests && /usr/bin/c++ -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -g -O2 -ffile-prefix-map=/build/openstructure-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/openstructure-2.3.1/modules/geom/tests/tests.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/alg/tests/test_fft.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/alg/src/CMakeFiles/ost_seq_alg.dir/build.make modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/DependInfo.cmake --color= 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::ResidueBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void mol_base::throw_invalid_chain_handle::test_method()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:114:18: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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/openstructure-2.3.1/obj-aarch64-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 file included from /usr/include/c++/12/string: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::ResidueBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void mol_base::throw_invalid_chain_handle::test_method()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_chain.cc:114:18: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void mol_base::throw_invalid_chain_handle::test_method()' at /build/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:365:38, inlined from 'void mol_base::throw_invalid_chain_handle::test_method()' at /build/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(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' 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); | ^~~~ make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/seq/alg/src/CMakeFiles/ost_seq_alg.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 27%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/seq/base/pymod/CMakeFiles/_ost_seq.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 28%] Built target _ost_seq [ 28%] Building CXX object modules/seq/base/tests/CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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_alignment.cc.o -MF CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o.d -o CMakeFiles/ost_seq_tests.dir/test_alignment.cc.o -c /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:28: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/openstructure-2.3.1/modules/seq/base/tests/test_aligned_region.cc:29: /build/openstructure-2.3.1/obj-aarch64-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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_profile.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/seq/base/tests/test_profile.cc [ 28%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_conn.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/base/tests/test_conn.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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_image_state_visitor.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.cc [ 28%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_index.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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_index.cc.o -MF CMakeFiles/ost_img_tests.dir/test_index.cc.o.d -o CMakeFiles/ost_img_tests.dir/test_index.cc.o -c /build/openstructure-2.3.1/modules/img/base/tests/test_index.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:24: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/aligned_region.hh:27, from /build/openstructure-2.3.1/modules/seq/base/tests/test_alignment.cc:25: /build/openstructure-2.3.1/obj-aarch64-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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 32%] running checks for module base cd /build/openstructure-2.3.1/modules/base/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage /build/openstructure-2.3.1/obj-aarch64-linux-gnu/tests/ost_base_tests Running 5 test cases... *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 32%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/bindings/pymod/CMakeFiles/_ost_bindings.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 32%] Built target _ost_bindings 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/tests/CMakeFiles/ost_conop_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 32%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/test_amino_acids.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/conop/tests/test_amino_acids.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_impl.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_def.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state.hh:31, from /build/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/modules/img/base/tests/test_image_state_visitor.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/seq/base/tests/CMakeFiles/ost_seq_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/seq/base/tests/tests.cc [ 34%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_fill.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/alg/tests/test_fill.cc [ 34%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_filter.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/alg/tests/test_filter.cc [ 34%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_coord_group.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/base/tests/test_coord_group.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/conop/amino_acids.hh:26, from /build/openstructure-2.3.1/modules/conop/tests/test_amino_acids.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-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/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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_filter.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_coord_group.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/algorithm.hh:32, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/alg/histogram.hh:30, from /build/openstructure-2.3.1/modules/img/alg/tests/test_histogram.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/img/base/tests/CMakeFiles/ost_img_tests.dir/test_sampling.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/base/tests/test_sampling.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/modules/img/base/tests/test_point.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/modules/img/base/tests/test_point.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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%] Linking CXX executable ../../../../tests/ost_seq_tests cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_seq.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so ../../../../stage/lib/libost_mol.so.2.3.1 ../../../../stage/lib/libost_info.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_regex.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 [ 35%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_mirror.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/alg/tests/test_mirror.cc make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 35%] Built target ost_seq_tests 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests/CMakeFiles/ost_geom_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 35%] running checks for module geom cd /build/openstructure-2.3.1/modules/geom/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage /build/openstructure-2.3.1/obj-aarch64-linux-gnu/tests/ost_geom_tests Running 25 test cases... *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 35%] Built target ost_geom_tests_run 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/base/tests/CMakeFiles/ost_seq_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 35%] running checks for module seq cd /build/openstructure-2.3.1/modules/seq/base/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage /build/openstructure-2.3.1/obj-aarch64-linux-gnu/tests/ost_seq_tests Running 32 test cases... *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 35%] Built target ost_seq_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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/seq/alg/pymod/CMakeFiles/_ost_seq_alg.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 35%] Built target _ost_seq_alg make -f modules/gfx/src/CMakeFiles/ost_gfx.dir/build.make modules/gfx/src/CMakeFiles/ost_gfx.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/src/CMakeFiles/ost_gfx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/gfx/src/CMakeFiles/ost_gfx.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 41%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/pymod/CMakeFiles/_ost_conop.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/conop/pymod/CMakeFiles/_ost_conop.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 42%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/src/CMakeFiles/ost_io.dir/DependInfo.cmake --color= [ 42%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_domains.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/base/tests/test_domains.cc make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/io/src/CMakeFiles/ost_io.dir/build.make modules/io/src/CMakeFiles/ost_io.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/io/src/CMakeFiles/ost_io.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 47%] Built target ost_io make -f modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build.make modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/alg/pymod/CMakeFiles/_ost_mol_alg.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 48%] Built target _ost_mol_alg make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/build.make modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 48%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/tests.cc.o -MF CMakeFiles/ost_gfx_tests.dir/tests.cc.o.d -o CMakeFiles/ost_gfx_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/gfx/tests/tests.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/pixel_sampling.hh:32, from /build/openstructure-2.3.1/modules/img/base/tests/test_sampling.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/modules/img/base/tests/test_sampling.hh:29, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_negate.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/alg/tests/test_negate.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_mirror.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_builder.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/base/tests/test_builder.cc [ 48%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_size.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/base/tests/test_size.cc [ 49%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_gfx_node.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/gfx/tests/test_gfx_node.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_state/image_state_spatial_domain.hh:31, from /build/openstructure-2.3.1/modules/img/base/tests/test_domains.cc:31: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_negate.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/conop/tests/CMakeFiles/ost_conop_tests.dir/test_heuristic_conop.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/conop/tests/test_heuristic_conop.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/builder.hh:26, from /build/openstructure-2.3.1/modules/mol/base/tests/test_builder.cc:22: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_power_spectrum.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/alg/tests/test_power_spectrum.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object_base.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_object.hh:40, from /build/openstructure-2.3.1/modules/gfx/tests/test_gfx_node.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/gfx_node.hh:26, from /build/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 50%] Building CXX object modules/img/base/tests/CMakeFiles/ost_img_tests.dir/test_value_holder.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/base/tests/test_value_holder.cc [ 50%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_shift.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/alg/tests/test_shift.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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/tests/CMakeFiles/ost_io_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 51%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_clustal.cc.o In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/conop/tests/test_heuristic_conop.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/log.hh:22, from /build/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 | ^~~~~~~~ cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/io/tests/test_clustal.cc /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_power_spectrum.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/clustal_io_handler.hh:25, from /build/openstructure-2.3.1/modules/io/tests/test_clustal.cc:27: /build/openstructure-2.3.1/obj-aarch64-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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_shift.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/img/base/tests/CMakeFiles/ost_img_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/base/tests/tests.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_stat.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/alg/tests/test_stat.cc [ 51%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_delete.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/base/tests/test_delete.cc [ 51%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_transform.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/alg/tests/test_transform.cc [ 51%] Linking CXX executable ../../../../tests/ost_img_tests cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 51%] Built target ost_img_tests 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 51%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_superposition.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/alg/tests/test_superposition.cc [ 51%] Building CXX object modules/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/test_normalizer.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/alg/tests/test_normalizer.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_stat.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/tests/CMakeFiles/ost_io_tests.dir/test_io_pdb.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc [ 51%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_color.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/gfx/tests/test_color.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_delete.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/conop/tests/CMakeFiles/ost_conop_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/conop/tests/tests.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_transform.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/svd_superpose.hh:27, from /build/openstructure-2.3.1/modules/mol/alg/tests/test_superposition.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/modules/img/alg/tests/test_normalizer.cc:35: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/color.hh:31, from /build/openstructure-2.3.1/modules/gfx/tests/test_color.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec_mat_predicates.hh:28, from /build/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/conop/tests/CMakeFiles/ost_conop_tests.dir/test_rule_based_conop.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/conop/tests/test_rule_based_conop.cc [ 51%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_entity.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/base/tests/test_entity.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/io/tests/test_io_pdb.cc:33: /build/openstructure-2.3.1/obj-aarch64-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/img/alg/tests/CMakeFiles/ost_img_alg_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/img/alg/tests/tests.cc [ 52%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_ics.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/base/tests/test_ics.cc [ 52%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_query.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/base/tests/test_query.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/conop/tests/test_rule_based_conop.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/vec_mat_predicates.hh:28, from /build/openstructure-2.3.1/modules/mol/base/tests/test_entity.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 52%] Linking CXX executable ../../../../tests/ost_img_alg_tests cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_img_alg.so.2.3.1 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 [ 52%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/alg/tests/tests.cc make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 52%] Built target ost_img_alg_tests make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build.make modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/mm/src/CMakeFiles/ost_mol_mm.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 53%] Built target ost_mol_mm 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 53%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_distance_analysis.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_ics.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/modules/mol/base/tests/test_entity.cc: In member function 'void mol_base::minmax::test_method()': /build/openstructure-2.3.1/modules/mol/base/tests/test_entity.cc:438:66: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 438 | std::pair minmax = ev.GetMinMax("test", Prop::ATOM); | ^ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 53%] Building CXX object modules/gfx/tests/CMakeFiles/ost_gfx_tests.dir/test_map_octree.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/gfx/tests/test_map_octree.cc [ 53%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_consistency_checks.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/alg/tests/test_consistency_checks.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc:28: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/clip_alignment.hh:27, from /build/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc:30: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/local_dist_diff_test.hh:26, from /build/openstructure-2.3.1/modules/seq/alg/tests/test_distance_analysis.cc:34: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh: In member function 'std::pair ost::mol::alg::StereoChemicalBondViolation::GetAllowedRange() const': /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/filter_clashes.hh:91:48: note: parameter passing for argument of type 'std::pair' when C++17 is enabled changed to match C++14 in GCC 10.1 91 | std::pair GetAllowedRange() const { return allowed_range_; } | ^ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/data.hh:36, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image_handle.hh:38, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/gfx/impl/map_octree.hh:22, from /build/openstructure-2.3.1/modules/gfx/tests/test_map_octree.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/alg/tests/test_consistency_checks.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 53%] Building CXX object modules/conop/tests/CMakeFiles/ost_conop_tests.dir/helper.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/conop/tests/helper.cc [ 53%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_surface.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/base/tests/test_surface.cc [ 53%] Building CXX object modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests.dir/test_partial_sec_struct_assignment.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/xcs_editor.hh:26, from /build/openstructure-2.3.1/modules/conop/tests/helper.cc:3: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 53%] Linking CXX executable ../../../tests/ost_gfx_tests cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-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/aarch64-linux-gnu/libOpenGL.so /usr/lib/aarch64-linux-gnu/libGLX.so /usr/lib/aarch64-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/aarch64-linux-gnu/libsqlite3.so ../../../stage/lib/libost_img_alg.so.2.3.1 ../../../stage/lib/libost_img.so.2.3.1 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 53%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/gfx/pymod/CMakeFiles/_ost_gfx.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 56%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/src/CMakeFiles/ost_gui.dir/DependInfo.cmake --color= 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 = 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::ChainBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:36:21: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:30: /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /usr/include/c++/12/string: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::ChainBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:36:21: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /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::ChainBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:36:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /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::ChainBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:36:21: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:38:19: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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 'ost::mol::EntityHandle make_query_test_entity()': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:38:19: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:38:19: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:38:19: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:40:18: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::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 'ost::mol::EntityHandle make_query_test_entity()': /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::AtomBase]' at /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:40:18: /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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_)))[16]' may be used uninitialized [-Wmaybe-uninitialized] 354 | __c1 = __c2; | ^~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:40:18: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/generic_property.hh:358:38, inlined from 'ost::mol::EntityHandle make_query_test_entity()' at /build/openstructure-2.3.1/modules/mol/base/tests/test_query.cc:40:18: /usr/include/c++/12/bits/basic_string.h:1071:16: warning: '*(const __vector(2) long 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<32, 8>::.boost::detail::aligned_storage::aligned_storage_imp<32, 8>::data_) + 8)' may be used uninitialized [-Wmaybe-uninitialized] 1071 | { return _M_string_length; } | ^~~~~~~~~~~~~~~~ /usr/include/boost/variant/variant.hpp: In function 'ost::mol::EntityHandle make_query_test_entity()': /usr/include/boost/variant/variant.hpp:2107:21: note: 'temp' declared here 2107 | variant temp(rhs); | ^~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_prop.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/surface_handle.hh:24, from /build/openstructure-2.3.1/modules/mol/base/tests/test_surface.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/gui/src/CMakeFiles/ost_gui.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 89%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/pymod/CMakeFiles/_ost_io.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/io/pymod/CMakeFiles/_ost_io.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 90%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/tests/CMakeFiles/ost_gfx_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 90%] running checks for module gfx cd /build/openstructure-2.3.1/modules/gfx/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage /build/openstructure-2.3.1/obj-aarch64-linux-gnu/tests/ost_gfx_tests In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/alg/sec_struct.hh:25, from /build/openstructure-2.3.1/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/mol/alg/tests/test_partial_sec_struct_assignment.cc:25: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 90%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_residue.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/base/tests/test_residue.cc [ 90%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_merge_pairwise_alignments.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/seq/alg/tests/test_merge_pairwise_alignments.cc [ 90%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/base/tests/test_view.cc [ 90%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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_transfer_connectivity.cc.o -MF CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o.d -o CMakeFiles/ost_mol_tests.dir/test_transfer_connectivity.cc.o -c /build/openstructure-2.3.1/modules/mol/base/tests/test_transfer_connectivity.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_residue.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 90%] Linking CXX executable ../../../../tests/ost_mol_alg_tests cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_alg_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_program_options.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-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/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-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/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libsqlite3.so ../../../../stage/lib/libost_base.so.2.3.1 ../../../../stage/lib/libost_geom.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/merge_pairwise_alignments.hh:22, from /build/openstructure-2.3.1/modules/seq/alg/tests/test_merge_pairwise_alignments.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 90%] Built target ost_mol_alg_tests 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/base/tests/CMakeFiles/ost_img_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 90%] running checks for module img cd /build/openstructure-2.3.1/modules/img/base/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage /build/openstructure-2.3.1/obj-aarch64-linux-gnu/tests/ost_img_tests Running 44 test cases... *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 90%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/img/alg/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/img/alg/tests/CMakeFiles/ost_img_alg_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 90%] running checks for module img_alg cd /build/openstructure-2.3.1/modules/img/alg/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage /build/openstructure-2.3.1/obj-aarch64-linux-gnu/tests/ost_img_alg_tests Running 25 test cases... *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 90%] Built target ost_img_alg_tests_run make -f modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/build.make modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/alg/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/build.make modules/mol/alg/tests/CMakeFiles/ost_mol_alg_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 90%] running checks for module mol_alg cd /build/openstructure-2.3.1/modules/mol/alg/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage /build/openstructure-2.3.1/obj-aarch64-linux-gnu/tests/ost_mol_alg_tests Running 4 test cases... *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 90%] Built target ost_mol_alg_tests_run make -f modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/build.make modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/build.make modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 90%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_interaction.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_interaction.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_view.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/builder.hh:26, from /build/openstructure-2.3.1/modules/mol/base/tests/test_transfer_connectivity.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 25 | class 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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/base.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/module_config.hh:22, from /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_interaction.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/modules/mol/mm/tests/test_interaction.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 90%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/test_view_op.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/base/tests/test_view_op.cc [ 90%] Building CXX object modules/mol/base/tests/CMakeFiles/ost_mol_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/mol/base/tests/tests.cc [ 91%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/test_sequence_identity.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/seq/alg/tests/test_sequence_identity.cc [ 91%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_crd.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/io/tests/test_io_crd.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/mol/base/tests/test_view_op.cc:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 91%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_dcd.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/io/tests/test_io_dcd.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alg/sequence_identity.hh:26, from /build/openstructure-2.3.1/modules/seq/alg/tests/test_sequence_identity.cc:25: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/alignment_handle.hh:29: /build/openstructure-2.3.1/obj-aarch64-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 | ^~~~~~~~ [ 91%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sdf.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/io/tests/test_io_sdf.cc [ 92%] Linking CXX executable ../../../tests/ost_conop_tests cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-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/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 92%] Built target ost_conop_tests make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build.make modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/mol/mm/pymod/CMakeFiles/_ost_mol_mm.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 93%] Built target _ost_mol_mm make -f modules/gui/pymod/CMakeFiles/_ost_gui.dir/build.make modules/gui/pymod/CMakeFiles/_ost_gui.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gui/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gui/pymod/CMakeFiles/_ost_gui.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Nothing to be done for 'modules/gui/pymod/CMakeFiles/_ost_gui.dir/build'. make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] Built target _ost_gui make -f modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/build.make modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/build.make modules/conop/tests/CMakeFiles/ost_conop_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] running checks for module conop cd /build/openstructure-2.3.1/modules/conop/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage /build/openstructure-2.3.1/obj-aarch64-linux-gnu/tests/ost_conop_tests Running 16 test cases... unable to open database file unable to open database file unable to open database file unable to open database file unable to open database file unable to open database file unable to open database file unable to open database file *** No errors detected make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] Built target ost_conop_tests_run make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts/CMakeFiles/ost_scripts.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f scripts/CMakeFiles/ost_scripts.dir/build.make scripts/CMakeFiles/ost_scripts.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_config /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/openstructure/libexec/ost_config cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/bin/ost cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different dng /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/bin/dng cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different ost_startup.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/ost_startup.py cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/scripts && /usr/bin/cmake -E copy_if_different /build/openstructure-2.3.1/scripts/dng_startup.py /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages//ost/dng_startup.py In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/io/tests/test_io_crd.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/seq/alg/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/seq/alg/tests/CMakeFiles/test_aaindex.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] running checks test_aaindex.py cd /build/openstructure-2.3.1/modules/seq/alg/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/seq/alg/tests/test_aaindex.py" . ---------------------------------------------------------------------- Ran 1 test in 1.042s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/tests/CMakeFiles/test_stutil.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] running checks test_stutil.py cd /build/openstructure-2.3.1/modules/base/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/base/tests/test_stutil.py" In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_frame.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_source.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/coord_group.hh:29, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/dcd_io.hh:28, from /build/openstructure-2.3.1/modules/io/tests/test_io_dcd.cc:23: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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 6 tests in 0.001s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/tests/CMakeFiles/test_table.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] running checks test_table.py cd /build/openstructure-2.3.1/modules/base/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/base/tests/test_table.py" ....................................../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 ../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/openstructure-2.3.1/obj-aarch64-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 26.752s OK [ 95%] Building CXX object modules/seq/alg/tests/CMakeFiles/ost_seq_alg_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/seq/alg/tests/tests.cc make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] Built target test_table.py_run 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/base/tests/CMakeFiles/test_log.py_run.dir/DependInfo.cmake --color= In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/io/tests/test_io_sdf.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] running checks test_log.py cd /build/openstructure-2.3.1/modules/base/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/base/tests/test_log.py" .... ---------------------------------------------------------------------- Ran 4 tests in 0.014s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests/CMakeFiles/test_msms.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] running checks test_msms.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_msms.py" Could not find msms executable: ignoring unit tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests/CMakeFiles/test_clustalw.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] running checks test_clustalw.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_clustalw.py" .[ 95%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_sequence_profile.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/io/tests/test_io_sequence_profile.cc ...... ---------------------------------------------------------------------- Ran 7 tests in 10.648s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] Built target test_clustalw.py_run 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]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests/CMakeFiles/test_hhblits.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] running checks test_hhblits.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_hhblits.py" [ 95%] Linking CXX executable ../../../../tests/ost_seq_alg_tests cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-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/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so No HHblits installation found: skip unit tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests/CMakeFiles/test_blast.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] running checks test_blast.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_blast.py" make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] Built target ost_seq_alg_tests make -f modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/depend Could not find blast executable: ignoring unit tests make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests/CMakeFiles/test_kclust.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] running checks test_kclust.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_kclust.py" make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 95%] Built target test_blast.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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests/CMakeFiles/test_naccess.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] running checks test_naccess.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_naccess.py" [ 96%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_block.cc Could not find kClust executable: ignoring unit tests Could not find NACCESS, could not test binding... make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] 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/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests/CMakeFiles/test_cadscore.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] running checks test_cadscore.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_cadscore.py" [ 96%] Built target test_kclust.py_run make -f modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_tmtools.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] running checks test_tmtools.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_tmtools.py" ... ---------------------------------------------------------------------- Ran 2 tests in 0.636s OK Could not find tmalign executable: ignoring unit tests Could not find tmalign executable: ignoring unit tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] Built target test_tmtools.py_run make -f modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_ialign.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] running checks test_ialign.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_ialign.py" . ---------------------------------------------------------------------- Ran 1 test in 0.337s OK Could not find ialign master perl script: ignoring unit tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] Built target test_ialign.py_run make -f modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_lga.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] running checks test_lga.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_lga.py" In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/load.hh:27, from /build/openstructure-2.3.1/modules/io/tests/test_io_sequence_profile.cc:29: /build/openstructure-2.3.1/obj-aarch64-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/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 | ^~~~~~~~ . ---------------------------------------------------------------------- Ran 1 test in 0.382s OK Could not find lga executable: ignoring unit tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] Built target test_lga.py_run make -f modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/DependInfo.cmake --color= [ 96%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_pir.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/io/tests/test_pir.cc make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/build.make modules/bindings/tests/CMakeFiles/test_hbplus.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] running checks test_hbplus.py cd /build/openstructure-2.3.1/modules/bindings/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/bindings/tests/test_hbplus.py" Could not find hbplus, could not test binding... make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] Built target test_hbplus.py_run make -f modules/conop/tests/CMakeFiles/test_processor.py_run.dir/build.make modules/conop/tests/CMakeFiles/test_processor.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/conop/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/conop/tests/CMakeFiles/test_processor.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/conop/tests/CMakeFiles/test_processor.py_run.dir/build.make modules/conop/tests/CMakeFiles/test_processor.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] running checks test_processor.py cd /build/openstructure-2.3.1/modules/conop/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/conop/tests/test_processor.py" In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_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 1 test in 0.001s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] Built target test_processor.py_run make -f modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/build.make modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/db/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/build.make modules/db/tests/CMakeFiles/test_linear_db.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] running checks test_linear_db.py cd /build/openstructure-2.3.1/modules/db/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/db/tests/test_linear_db.py" ... ---------------------------------------------------------------------- Ran 3 tests in 0.046s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] Built target test_linear_db.py_run make -f modules/geom/tests/CMakeFiles/test_geom.py_run.dir/build.make modules/geom/tests/CMakeFiles/test_geom.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/geom/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/geom/tests/CMakeFiles/test_geom.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/geom/tests/CMakeFiles/test_geom.py_run.dir/build.make modules/geom/tests/CMakeFiles/test_geom.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] running checks test_geom.py cd /build/openstructure-2.3.1/modules/geom/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/geom/tests/test_geom.py" ........ ---------------------------------------------------------------------- Ran 8 tests in 0.019s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 96%] Built target test_geom.py_run make -f modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/build.make modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/gfx/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/build.make modules/gfx/tests/CMakeFiles/test_gfx.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 97%] running checks test_gfx.py cd /build/openstructure-2.3.1/modules/gfx/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/gfx/tests/test_gfx.py" ...... ---------------------------------------------------------------------- Ran 6 tests in 0.016s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 97%] Built target test_gfx.py_run make -f modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_pdb.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 97%] running checks test_io_pdb.py cd /build/openstructure-2.3.1/modules/io/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/io/tests/test_io_pdb.py" ...s ---------------------------------------------------------------------- Ran 4 tests in 0.039s OK (skipped=1) make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 97%] Built target test_io_pdb.py_run [ 97%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_iomanager.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/io/tests/test_iomanager.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_block.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/modules/mol/mm/tests/test_block.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/pir_io_handler.hh:25, from /build/openstructure-2.3.1/modules/io/tests/test_pir.cc:27: /build/openstructure-2.3.1/obj-aarch64-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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/seq/sequence_io_handler.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/io_manager.hh:28, from /build/openstructure-2.3.1/modules/io/tests/test_iomanager.cc:22: /build/openstructure-2.3.1/obj-aarch64-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/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 | ^~~~~~~~ [ 97%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/io/tests/tests.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ [ 97%] Linking CXX executable ../../../../tests/ost_mol_tests cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 97%] Built target ost_mol_tests make -f modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_mmcif.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 97%] running checks test_io_mmcif.py cd /build/openstructure-2.3.1/modules/io/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/io/tests/test_io_mmcif.py" .........s ---------------------------------------------------------------------- Ran 10 tests in 12.346s OK (skipped=1) make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 97%] Built target test_io_mmcif.py_run make -f modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/io/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/build.make modules/io/tests/CMakeFiles/test_io_omf.py_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 97%] running checks test_io_omf.py cd /build/openstructure-2.3.1/modules/io/tests && sh -c "PYTHONPATH=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib/python3.11/dist-packages/ /usr/bin/python3 /build/openstructure-2.3.1/modules/io/tests/test_io_omf.py" [ 97%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_star_parser.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/io/tests/test_star_parser.cc . ---------------------------------------------------------------------- Ran 1 test in 7.403s OK make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 97%] Built target test_io_omf.py_run make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/depend make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu && /usr/bin/cmake -E cmake_depends "Unix Makefiles" /build/openstructure-2.3.1 /build/openstructure-2.3.1/modules/mol/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/tests /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/DependInfo.cmake --color= make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make -f modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build.make modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build make[4]: Entering directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 97%] running checks for module mol cd /build/openstructure-2.3.1/modules/mol/base/tests && env OST_ROOT=/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage /build/openstructure-2.3.1/obj-aarch64-linux-gnu/tests/ost_mol_tests Running 70 test cases... ./modules/mol/base/tests/test_ics.cc(216): error: in "mol_base/ics_settorsion_linear_unbuffered": difference{4} between s.t2.GetAngle(){-2.3561945} and Real(3.14159265358979323846/4){0.785398185} exceeds 0.0001% *** 1 failure is detected in the test module "ost_mol_base" make[4]: *** [modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/build.make:74: modules/mol/base/tests/CMakeFiles/ost_mol_tests_run] Error 201 make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' make[3]: *** [CMakeFiles/Makefile2:5237: modules/mol/base/tests/CMakeFiles/ost_mol_tests_run.dir/all] Error 2 make[3]: *** Waiting for unfinished jobs.... [ 98%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_reader.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/io/tests/test_mmcif_reader.cc [ 98%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_mmcif_info.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/io/tests/test_mmcif_info.cc [ 98%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_io_img.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/io/tests/test_io_img.cc [ 98%] Building CXX object modules/io/tests/CMakeFiles/ost_io_tests.dir/test_exceptions.cc.o cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/openstructure-2.3.1/modules/io/tests/test_exceptions.cc [ 98%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_block_modifiers.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:24, from /build/openstructure-2.3.1/modules/io/tests/test_mmcif_reader.cc:26: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_reader.hh:25: /build/openstructure-2.3.1/obj-aarch64-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/mmcif_info.hh:25, from /build/openstructure-2.3.1/modules/io/tests/test_mmcif_info.cc:24: /build/openstructure-2.3.1/obj-aarch64-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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/entity_handle.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mol.hh:22, from /build/openstructure-2.3.1/modules/io/tests/test_star_parser.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_view.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_handle.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:24: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/map.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/load_map.hh:24, from /build/openstructure-2.3.1/modules/io/tests/test_io_img.cc:29: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/vecmat.hh:33, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/point.hh:35, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/image.hh:34, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/img/map.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/img/load_map.hh:24, from /build/openstructure-2.3.1/modules/io/tests/test_exceptions.cc:27: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/interaction.hh:34, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_block_modifiers.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/modules/mol/mm/tests/test_block_modifiers.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : 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/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_topology.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology.hh:31, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_topology.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/modules/mol/mm/tests/test_topology.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : 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/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_forcefield.cc . ---------------------------------------------------------------------- Ran 2 tests in 295.713s OK Could not find CAD score classic executables: ignoring unit tests make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [ 98%] Built target test_cadscore.py_run [ 98%] Building CXX object modules/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/test_simulation.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/modeller.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/topology_creator.hh:37, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_topology.cc:22: /build/openstructure-2.3.1/obj-aarch64-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/mol/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/tests && /usr/bin/c++ -DQT_CORE_LIB -DQT_GUI_LIB -DQT_NO_DEBUG -DQT_WIDGETS_LIB -DQT_XML_LIB -I/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include -I/usr/include/eigen3 -isystem /usr/include/aarch64-linux-gnu/qt5 -isystem /usr/include/aarch64-linux-gnu/qt5/QtXml -isystem /usr/include/aarch64-linux-gnu/qt5/QtCore -isystem /usr/lib/aarch64-linux-gnu/qt5/mkspecs/linux-g++ -isystem /usr/include/aarch64-linux-gnu/qt5/QtGui -isystem /usr/include/aarch64-linux-gnu/qt5/QtWidgets -g -O2 -ffile-prefix-map=/build/openstructure-2.3.1=. -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/mm/tests/CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o -MF CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o.d -o CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o -c /build/openstructure-2.3.1/modules/mol/mm/tests/tests.cc In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/settings.hh:31, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_forcefield.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/modules/mol/mm/tests/test_forcefield.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite2.hh:27, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/composite.hh:22, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/geom.hh:28, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query_state.hh:26, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/query.hh:39, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/residue_handle.hh:25, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/mol/mm/settings.hh:31, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_simulation.cc:21: /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:25:41: warning: '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/openstructure-2.3.1/modules/mol/mm/tests/test_simulation.cc:20: /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/geom/circular_iterator.hh:100:35: warning: 'template struct std::iterator' is deprecated [-Wdeprecated-declarations] 100 | class circular_iter : public std::iterator | ^~~~~~~~ /usr/include/c++/12/bits/stl_iterator_base_types.h:127:34: note: declared here 127 | struct _GLIBCXX17_DEPRECATED iterator | ^~~~~~~~ In file included from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/seq/sequence_list.hh:23, from /build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/include/ost/io/mol/pdb_reader.hh:28, from /build/openstructure-2.3.1/modules/mol/mm/tests/test_simulation.cc:29: /build/openstructure-2.3.1/obj-aarch64-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%] Linking CXX executable ../../../tests/ost_io_tests cd /build/openstructure-2.3.1/obj-aarch64-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/openstructure-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/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-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/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_program_options.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [100%] Built target ost_io_tests [100%] Linking CXX executable ../../../../tests/ost_mol_mm_tests cd /build/openstructure-2.3.1/obj-aarch64-linux-gnu/modules/mol/mm/tests && /usr/bin/cmake -E cmake_link_script CMakeFiles/ost_mol_mm_tests.dir/link.txt --verbose=1 /usr/bin/c++ -g -O2 -ffile-prefix-map=/build/openstructure-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_mm_tests.dir/test_interaction.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_block.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_block_modifiers.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_topology.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_forcefield.cc.o CMakeFiles/ost_mol_mm_tests.dir/test_simulation.cc.o CMakeFiles/ost_mol_mm_tests.dir/tests.cc.o -o ../../../../tests/ost_mol_mm_tests -L/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib -Wl,-rpath,/build/openstructure-2.3.1/obj-aarch64-linux-gnu/stage/lib /usr/lib/aarch64-linux-gnu/libboost_unit_test_framework.so ../../../../stage/lib/libost_mol_mm.so.2.3.1 ../../../../stage/lib/libost_io.so.2.3.1 ../../../../stage/lib/libost_mol_alg.so.2.3.1 /usr/lib/aarch64-linux-gnu/libboost_program_options.so ../../../../stage/lib/libost_conop.so.2.3.1 ../../../../stage/lib/libost_db.so.2.3.1 /usr/lib/aarch64-linux-gnu/libsqlite3.so /usr/lib/aarch64-linux-gnu/libboost_thread.so /usr/lib/aarch64-linux-gnu/libboost_chrono.so /usr/lib/aarch64-linux-gnu/libboost_date_time.so /usr/lib/aarch64-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/aarch64-linux-gnu/libboost_filesystem.so /usr/lib/aarch64-linux-gnu/libboost_system.so /usr/lib/aarch64-linux-gnu/libQt5Xml.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Widgets.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Gui.so.5.15.8 /usr/lib/aarch64-linux-gnu/libQt5Core.so.5.15.8 /usr/lib/aarch64-linux-gnu/libfftw3f.so /usr/lib/aarch64-linux-gnu/libfftw3f_threads.so /usr/lib/aarch64-linux-gnu/libboost_iostreams.so /usr/lib/aarch64-linux-gnu/libboost_regex.so /usr/lib/aarch64-linux-gnu/libtiff.so /usr/lib/aarch64-linux-gnu/libpng.so /usr/lib/aarch64-linux-gnu/libz.so /usr/lib/aarch64-linux-gnu/libOpenMM.so make[4]: Leaving directory '/build/openstructure-2.3.1/obj-aarch64-linux-gnu' [100%] Built target ost_mol_mm_tests Thu Jun 8 18:26:11 UTC 2023 - pbuilder was killed by timeout after 18h.